The microbial endogenous respiration process is very important in biological water treatment processes. This study analyzed and compared the endogenous respiration process in an attached growth membrane bioreactor (aMBR) system and a UV/O-3 integrated aMBR system (UV/O-3-aMBR) in treating polluted surface water with CODMn around 10 mg/L. The endogenous respiration activity of heterotrophic microbes and autotrophic nitrifiers activity in both systems was analyzed and compared. Results show that heterotrophic bacteria and autotrophic nitrifiers enter endogenous respiration at 6 h aeration in an aMBR and 0 h in a UV/O-3-aMBR system. Biomass amount on PVA-gel in aMBR was higher than in UV/O-3-aMBR in terms of specific respiration rates SOURt, SOURH, and SOURA. Substrate remained on PVA-gel in the aMBR system, but no substrate remained on PVA-gel in the UV/O-3-aMBR system. Higher species of microbes, including recoverable and irrecoverable components, existed in the aMBR system as compared to the UV/O-3-aMBR system. The UV/O-3-aMBR system could make full use of the advanced oxidation process (AOP) and biological process, leading to a higher treatment performance, and has the potential to mitigate total energy demand. Thus, the UV/O-3-aMBR system can be used as a new technology for treating polluted surface water with the co-contribution of biological process and AOP treatment.