@RequestMapping(value = "/add" , method = RequestMethod.GET)
public String add(Model model) {
    model.addAttribute("employee",new Employee());
    model.addAttribute("certificates",certificateService.getList());
    return "add";
}

@RequestMapping(value = "/add" , method = RequestMethod.POST)
public String addSave(@ModelAttribute("employee")Employee employee) {
    System.out.println(employee);
    return "list";
}

@Entity
@Table(name = "employee")
public class Employee {

@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
@Column(name = "ID")
private int id;

@Column(name = "Name")
private String name ;


@ManyToMany(fetch = FetchType.EAGER)
@JoinTable(name="emp_cert",
             joinColumns={@JoinColumn(name="employee_id")},
             inverseJoinColumns={@JoinColumn(name="certificate_id")})
private List<Certificate> certificates;



public Employee() {
    if(certificates == null)
         certificates = new ArrayList<>();
}

public int getId() {
    return id;
}

public void setId(int id) {
    this.id = id;
}

public String getName() {
    return name;
}


public void setName(String name) {
    this.name = name;
}


public List<Certificate> getCertificates() {
    return certificates;
}


public void setCertificates(List<Certificate> certificates) {
    this.certificates = certificates;
}

@Override
public String toString() {
    return "Employee [id=" + id + ", name=" + name + "certificates size = "+certificates.size()+" ]";
}


@Entity
@Table(name = "certificate")
public class Certificate {

@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
@Column(name = "Id")
private int id;

@Column(name = "name")
private String name ;


@ManyToMany(mappedBy="certificates")
private List<Employee> employees ;


public Certificate() {
   if(employees == null)
       employees = new ArrayList<>();
}

public int getId() {
    return id;
}

public void setId(int id) {
    this.id = id;
}

public String getName() {
    return name;
}

public void setName(String name) {
    this.name = name;
}

public List<Employee> getEmployees() {
    return employees;
}

public void setEmployees(List<Employee> employees) {
    this.employees = employees;
}

@Override
public int hashCode() {
    final int prime = 31;
    int result = 1;
    result = prime * result + id;
    return result;
}

@Override
public boolean equals(Object obj) {
    if (this == obj)
        return true;
    if (obj == null)
        return false;
    if (getClass() != obj.getClass())
        return false;
    Certificate other = (Certificate) obj;
    if (id != other.id)
        return false;
    return true;
}

<form action="#" th:action="@{/employee/add}" th:object="${employee}" method="post">
         <table>
           <tr>
             <td>Name</td>
             <td><input type="text" th:field="*{name}"></td>
           </tr>
           <tr>
             <td>Certificate</td>
             <td>
               <th:block th:each="certificate , stat : ${certificates}">
                 <input type="checkbox" th:field="*{certificates}" name="certificates" th:value="${certificate.id]}"/>
                 <label th:text="${certificate.name}" ></label>
               </th:block>
             </td>
           </tr>
           <tr>
           <td colspan="2">
              <input type="submit" value="Add"/></td>
           </tr>
         </table>
      </form>

<tr>
             <td>Certificate</td>
             <td>
               <th:block th:each="certificate : ${certificates}">
                <input type="checkbox" name="cers" th:value="${certificate.id}"/>
                 <label th:text="${certificate.name}"></label>
               </th:block>
             </td>
           </tr>

@RequestMapping(value = "/add" , method = RequestMethod.POST)
public String addSave(
         @ModelAttribute("employee")Employee employee ,
         @RequestParam(value = "cers" , required = false) int[] cers ,
         BindingResult bindingResult , Model model) {

if(cers != null) {
    Certificate certificate = null ;
    for (int i = 0; i < cers.length; i++) {

        if(certificateService.isFound(cers[i])) {
            certificate = new  Certificate();
            certificate.setId(cers[i]);
          employee.getCertificates().add(certificate);
        }
    }
        for (int i = 0; i < employee.getCertificates().size(); i++) {
            System.out.println(employee.getCertificates().get(i));
        }
}

<input type="checkbox" th:field="*{certificates}" name="certificates" th:value="${certificate.id]}"/>

<input type="checkbox" th:field="*{certificates}" name="certificates" th:value="${certificate.id}"/>