Low-flush toilets have received increasing attention in relation to the water crisis in water-scarce regions because the vacuum flushing system (VFS) can reduce the amount of water required for flushing by approximately 80%. However, low-flush toilet wastewater exhibits the characteristics of high pollutant concentrations and cannot be directly discharged into urban pipe networks; therefore, decentralized wastewater treatment is necessary. Traditional control process (mainly consisting of hydrolysis acidification tank (HAT), anaerobic-anoxic–oxic (AAO) tank, coagulation sedimentation filtration tank and UV disinfection) was unsatisfactory for treating this type of wastewater. Therefore, a newly designed integrated biological-electrocatalytic (AAIE) process (mainly consisting of anaerobic baffled reactor (ABR), alternating internal circulation activated sludge process (AICS), and electrocatalytic oxidation (EC)) was introduced. ABR achieved large amounts of organic matter removal, the organic biodegradation kinetics revealed that the maximum specific degradation rate of the ABR was 0.050 to 0.082 d−1; AICS further removed COD and nitrogen, the denitrification rate and growth rate of nitrifying bacteria in the AICS were in the range of 0.079–0.121 kg/(kg·d) and 0.32–1.54 d−1, respectively. The temperature and organic loading rate were identified as two key parameters for ABR and AICS to remove pollutants, therefore, EC was the guarantee to make the effluent quality met the directly discharge standard of China (GB 18918-2002), especially in winter. The results showed that the AAIE process presented COD, colority, ammonia and total nitrogen removal rates of 98.5 ± 0.7%, 98.8 ± 0.6%, 97.0 ± 0.4% and 93.4 ± 2.6%, respectively, which were considerably higher than those of the control process. Furthermore, the economic analysis indicated that the AAIE process was feasible and may help to pave the way for wide application of biological-electrocatalytic processes for highly concentrated toilet wastewater treatment.