In order to optimize the integrated treatment process of “air flotation/bio-ceramic/membrane” for the treatment of micro-polluted surface water, the effect of air flotation time, filtration rate, and membrane permeation rate on the removal of chlorophyll a and permanganate index (CODMn) were investigated by the response surface method (RSM), and the experimental factors were optimized by a quadratic regression equation and response surface. Quadratic regression equations and response surfaces optimized the experimental factors. The results showed that the air flotation time was positively correlated with the removal efficiency of chlorophyll a and CODMn. The effect of filtration rate on the removal of CODMn was more significant than that of chlorophyll a, and the impact of membrane permeation rate on the removal efficiency of both pollutants was not substantial. In the validation tests conducted when air flotation time was 30 min, the filtration rate was 3 m/h, the membrane permeation rate was 35 L/(m2·h), the total average removal efficiency of chlorophyll a was 94.15±3.38%, and the total average removal efficiency of CODMn was 72.17±2.58%, which were in good agreement with the model predictions.