php_value in .htaccess only work if you choose mod_php/_ruid2/_itk.
For php-fpm, modified '/home/php-fpm/tpl/custom.php53-fpm-pool.conf.tpl' (copy from php53-fpm-pool.conf.tpl) with add 'php_admin_value[max_input_vars] = 3000'. For suphp/fcgid, modified '/home/phpini/tpl/custom.php.ini.tpl' (copy from php.ini.tpl) with add 'max_input_vars = 3000'. After that run 'sh /script/fixphp' and then 'sh /script/restart-web'.