How to set DB_Database field in .env from controller at runtime in laravel 5.3?

Actually it's possible but it is not good idea. For switch between DB you can:

1.Add connection to your config/database.php file:

'connections' => [

    'mysql' => [
        'driver' => 'mysql',
        'host' => env('DB_HOST', 'localhost'),
        'port' => env('DB_PORT', '3306'),
        'database' => env('DB_DATABASE', 'forge'),
        'username' => env('DB_USERNAME', 'forge'),
        'password' => env('DB_PASSWORD', ''),
        'charset' => 'utf8',
        'collation' => 'utf8_unicode_ci',
        'prefix' => '',
        'strict' => true,
        'engine' => null,
    ],

    'mysql2' => [
        'driver' => 'mysql',
        'host' => env('DB_HOST', 'localhost'),
        'port' => env('DB_PORT', '3306'),
        'database' => env('DB_DATABASE', 'forge'),
        'username' => env('DB_USERNAME', 'forge'),
        'password' => env('DB_PASSWORD', ''),
        'charset' => 'utf8',
        'collation' => 'utf8_unicode_ci',
        'prefix' => '',
        'strict' => true,
        'engine' => null,
    ],

],

2.Specify connection for DB request:

$users = DB::connection('mysql')->select(...);
$users = DB::connection('mysql2')->select(...);