The invention relates to an intelligent control system for comprehensive utilization of rainwater and a control method of the intelligent control system. The intelligent control system comprises a remote computer central control platform, a rainfall sensor, a rainwater collection device, a rainwater discarding flow treatment device, a rainwater collection pool, a rainwater reuse lifting pump and a clean water pool, the rainwater collection device, the rainwater discharging flow treatment device, the rainwater collection pool, the rainwater reuse lifting pump and the clean water pool are connected sequentially through a pipeline, the clean water pool is connected with an afforestation sprinkling irrigation device and a garage flushing device through a middle water electric butterfly valve, the rainwater discarding flow treatment device is connected with a municipal sewer through a rainwater discharging flow electric butterfly valve, and liquid level meters in the rainwater collection pool and the clean water pool, the rainfall sensor, the rainwater reuse lifting pump and the above valves are connected with the remote computer central control platform respectively. The control method includes: collecting liquid level of each pool in real time; intelligently combining current realtime rainfall and subsequent possible weather condition; automatically analyzing and judging; automatically controlling start and stop of each stage of rainwater reuse. The intelligent control system is reasonable in control, rainwater utilization rate is increased, off-peak electricity can be utilized for rainwater treatment, and electric energy is saved.