A system and method for automatically flushing urine from a pet litter box are disclosed. In one embodiment, the system and method may be directed to a combination of a urine-separating pet litter box with odor controlling conditionally non-absorbent litter and an automatic flushing device. The urine-separating pet litter box includes an upper litter tray with a perforated bottom and a lower liquid holding tank, which holds water inside. The lower liquid holding tank is connected to water intake pipes and a drainpipe and flushes the urine and holding water and fills freshwater in the lower liquid holding tank by detecting a water level of the holding water in the lower liquid holding tank with sensors. The flushing was performed by using a Venturi pump effect to control two electrical valves open or close. In some embodiment, Sodium Sesquicarbonate (SSC) may be used as conditionally non-absorbent litter for complete disposal of feces.