$array = array(
    98 => array(
        'City' => 'Caracas',
        'Country' => 'Venezuela',
        'Continent' => 'Latin America',
    ),
    99 => array(
        'City' => 'Cairo',
        'Country' => 'Egypt',
        'Continent' => 'Middle East',
    ),
    105 => array(
        'City' => 'Abu Dhabi',
        'Country' => 'United Arab Emirates',
        'Continent' => 'Middle East',
    ),
    106 => array(
        'City' => 'Dubai',
        'Country' => 'United Arab Emirates',
        'Continent' => 'Middle East',
    ),
    107 => array(
        'City' => 'Montreal',
        'Country' => 'Canada',
        'Continent' => 'North America',
    )
);

$newArray = array();
foreach ($array as $row)
{
   $newArray[$row['Continent']][$row['Country']][] = $row['City'];
}

print_r($newArray);

还有几种替代方法：
在无主体的foreach()中使用“数组解构”来填充分层结构（Demo）（Further about the technique）

$result = [];
foreach (
    $array as
    [
        'Continent' => $a,
        'Country' => $b,
        'City' => $result[$a][$b][]
    ]
);
var_export($result);

使用array_reduce()避免在全局范围内声明结果变量。（Demo）

var_export(
    array_reduce(
        $array,
        function($result, $row) {
            $result[$row['Continent']][$row['Country']][] = $row['City'];
            return $result;
        }
    )
);

那么这个解决方案呢：

function arrayToMultiDimensionalArray(array $elements, array $dimensions)
{
    $output = [];

    foreach ($elements as $element) {
        $outputElement =& $output;

        // Foreach to build up the dimensions
        foreach ($dimensions as $dimension) {
            $outputElement =& $outputElement[$element[$dimension]];
        }

        $outputElement[] = $element['City'];
    }

    return $output;
}

$dimensions = ['Continent', 'Country'];

$tree = arrayToMultiDimensionalArray($array, $dimensions);

我认为你只需要在你的数组中循环，然后创建一个新的数组，使用一些值作为键，另一些值作为值，例如

$new_array = array();
foreach($array as $val)
{ 
     $new_array[$val['Continent']][$val['Country']] = array('City' => $val['City']);
}

Live Sample