您可以使用Joost提供的想法并使用upload_dir 筛选以临时将上载路径设置为其他位置。

/**
 * Override the default upload path.
 * 
 * @param   array   $dir
 * @return  array
 */
function wpse_141088_upload_dir( $dir ) {
    return array(
        \'path\'   => $dir[\'basedir\'] . \'/mycustomdir\',
        \'url\'    => $dir[\'baseurl\'] . \'/mycustomdir\',
        \'subdir\' => \'/mycustomdir\',
    ) + $dir;
}

// Register our path override.
add_filter( \'upload_dir\', \'wpse_141088_upload_dir\' );

// Do our thing. WordPress will move the file to \'uploads/mycustomdir\'.
$result = wp_handle_upload( $_FILE[\'myfile\'] );

// Set everything back to normal.
remove_filter( \'upload_dir\', \'wpse_141088_upload_dir\' );