$input = [ [1,2,3], [4,5,6], [7,8,9] ];

for ($i = 0; $i < count($input); $i++) {

$res[] = [
    array_shift($input[0]),
    array_shift($input[1]),
    array_shift($input[2])
                ];
}

//output
Array
(
    [0] => Array
        (
            [0] => 1
            [1] => 4
            [2] => 7
        )

    [1] => Array
        (
            [0] => 2
            [1] => 5
            [2] => 8
        )

    [2] => Array
        (
            [0] => 3
            [1] => 6
            [2] => 9
        )

)