The invention provides a patent fee withholding system and a method thereof. The patent fee withholding system comprises a background management system and a client connected with a business support module via networks, the background management system has functions of patent information inputting, checking, and screening, the client displays an information interface via a browser, the displayed information interface comprises a register module, a login module, a checking module, a screening module, and a payment module, and the business support module comprises a database, a data operation module, and a short message transmit-receive module with an auto-response function. The invention also provides a patent fee paying method based on the patent fee withholding system. By employing the patient fee withholding system and the method thereof, the workload for the clients can be greatly reduced, consequences of patent failure due to late fee payment or recovery of the patent right via the payment of right requirement recovery fees can be avoided, and the manual error cost is reduced to the maximum.