BACKGROUND: Due to its fast service and high utilization, day surgery is becoming more and more important in the medical system. As a result, an effective day surgery scheduling can reasonably release the supply and demand pressure. OBJECTIVE: This paper aims to investigate the day surgery scheduling problem with patient preferences and limited operation room for the sake of increasing operation efficiency and further decreasing surgery costs. METHODS: A multiple objective stochastic programming model is constructed to seek a satisfactory surgical scheduling for both patients and hospitals under different scenarios. Multi-objective genetic algorithm is designed to solve the model and different scales of scenarios are utilized to test the effectiveness of the algorithm and modeling process. RESULTS: Results show that the proposed model and algorithm can provide a feasible solution for maximizing individual preference of surgeons with surgery date and operation room utilization as well. CONCLUSIONS: Patient preference is proposed to be incorporated into day surgery scheduling, and the variability of surgery duration considered to seek a satisfactory surgery scheduling scheme for both patients and hospitals is more in line with the actual hospital situation.