The invention belongs to the technical field of automatic control, and relates to an anti-theft flow device control system and method. The system comprises an upper computer, an encryption / decryptiondevice, a controller, an execution mechanism group, a bus A, a bus B, a bus C and a software system, the software system comprises control software, a function module and a data link encryption / decryption module, and a user can only edit the control software and call the function module and cannot edit the data link encryption / decryption module. Encryption modes of the data link encryption / decryption module and the encryption / decryption device comprise an encryption baud rate, an encryption data frame format and an encryption data transmission protocol. The system can prevent software developers of a flow standard device control system development company from embezzling the control system and protect intellectual properties of the flow standard device control system development company.