The increasing water consumption in cities and towns makes the municipal sewage treatment in alpine and high altitude areas more and more difficult, and the optimization of the biochemical reaction effect of the reaction tanks in the sewage treatment process has become an important way to solve this problem. In this paper, starting from the structure of sewage treatment system in alpine and high altitude areas, based on the mathematical model of activated sludge method, its biological reaction process and multi-layer sedimentation model are analyzed. Then combined with MATLAB software, based on the model assumptions and the material balance equation of the concentration of each component in the reaction tank, the simulation model of the biodegradation process in the wastewater treatment reaction tank was constructed and the biochemical reaction under the change of the dosing ratio and temperature was analyzed through simulation. Then the outlet water quality and the total energy consumption of wastewater treatment were taken as the objective functions, and a multi-objective optimization model of wastewater treatment process was constructed, and the improved cuckoo search algorithm was introduced for optimization and solution. The results showed that when the value of input ratio was 0.008, the ammonia nitrogen concentration in the wastewater treatment reactor was stabilized in about 17 days and the concentration was less than 0.99 mg/L. By increasing the temperature to 36°C, the highest value of μH could be reached to 2.45 d-1, and the COD concentration of effluent could be controlled to about 49.96 mg/L. The results showed that the maximum value of μH could be reached to 2.45 d-1 by increasing the temperature to 36°C, and the COD concentration in the effluent could be controlled to about 49.96 mg/L. And the ICS algorithm can realize the optimal result solution of the multi-objective optimization model of wastewater treatment, which helps to improve the efficiency of wastewater treatment and reduce the energy consumption of wastewater treatment in alpine and high altitude areas.