A control system of an intelligent toilet includes a toilet seat actuation device for operating a toilet seat, a seat cover actuation device for operating a seat cover, and a control circuit which includes a user detector for detection of presence of a user and a micro-controller to actuate the toilet seat actuation device and the seat cover actuation device between a male operation mode and a female operation mode. In the male operation mode, the toilet seat actuation device and the seat cover actuation device are actuated for lifting up the toilet seat and the seat cover. In the female operation mode, the seat cover actuation device is actuated for lifting up the seat cover. The control system is convenient in use and prevents any contamination of the user' hands by touching the intelligent toilet.