Using reclaimed water to flush toilets could greatly reduce household water consumption. However, deterioration in the quality of reclaimed water, such as increased odor and bacterial growth, restrict its reuse. This study compared changes in residual chlorine, BOD5, NH3–N, turbidity, and color in four kinds of reclaimed water that can be reused for flushing household toilets. Bacterial reproduction and regeneration in the reclaimed water and the succession law of the microbial communities were also explored to reveal the influence of biofilm in the reclaimed water on the biological stability of the reclaimed water. The results show that under conditions of 30 °C after the addition of 6 mg/L of chlorine, no bacteria were discovered after 1 month, 20 days, or 10 days in the MBR effluent of greywater (GMBR), BAF effluent of greywater (GBAF), or reclaimed water of mixed domestic wastewater (MWR), respectively. The GMBR was similar to tap water, and was obviously better than the MWR. To control the proliferation of microorganisms, the recommend residual chlorine concentration should be no less than 0.80 mg/L at the point of use. However, when the concentration of residual chlorine in the reclaimed water was less than 0.9 mg/L (GMBR) or 1.5 mg/L (MWR), the chlorine could not kill the bacteria on the biofilm. Therefore, to control the biological stability of the reclaimed water, sufficient residual chlorine should be maintained, and the concentration of organic matter in the reclaimed water should be reduced as much as possible. Our findings showed that recycled greywater is more suitable for flushing household toilets than recycled mixed sewage.