Onsite separated-synergetic wastewater treatment (OSSWT) is a new sanitation system designed for decentralized housing, such as that found in rural areas. This study used four reactors to investigate the impact of the amount of flushed toilet water (AFTW) on partial nitritation/anammox (PN/A) in an OSSWT system. AFTW affects the endpoint of PN by impacting total alkalinity (TA). While the AFTW did not affect the average total ammonia nitrogen (TAN) reaction rate, it affected the type and proportion of activated sludge; high AFTW was not conducive to the growth of attached sludge. PN could be rebuilt by using a simple pause and resume aeration technique when AFTW was low. Increasing AFTW reduced Nitrosamonas abundance when AFTW was low, but this effect began to reverse when AFTW was high. The results of this study provide a reference for the application of PN-A on rural domestic sewage and can direct the reactor /process design of OSWWT.