public class MyYobaContext : DbContext, IMyYobaContext {
    public DbSet<SmallYoba> { get; set; }
    public DbSet<BigYoba> { get; set; }
    public DbSet<SmallBigYoba> { get; set; }

    protected override void OnModelCreating(ModelBuilder modelBuilder)
    {
        modelBuilder.Entity<SmallBigYoba>()
           .HasKey(option => new { option.SmallYobaId, option.BigYobaId });
            base.OnModelCreating(modelBuilder);
        base.OnModelCreating(modelBuilder);
    }
}

public class SmallBigYoba {
    public int SmallYobaId { get; set; }
    public SmallYoba SmallYoba { get; set; }

    public int BigYobaId { get; set; }
    public BigYoba BigYoba { get; set; }
}

public class BigYoba {
    ...
    ICollection<SmallBigYoba> ManyToManyYoba { get; set; }
    ...
}

public class SmallYoba {
    ...
    ICollection<SmallBigYoba> ManyToManyYoba { get; set; }
    ...
}