Faculty performance evaluation is an important element of assessment for departments and universities. A quantitative score is often needed for faculty annual evaluation, but its determination is often subjective and hard to incorporate the versatile contributions of individual faculty. Here, we propose a quantitative and objective faculty performance evaluation method. We established a quantitative scoring system which scored faculty performance in key activities using expectation-based formula on key measures and then incorporated personalized flexible weights to integrate them into overall scores. The scoring system was structured to evaluate annual faculty performance in the areas of teaching, research, service and overall. It was implemented in a programed Excel form, making it convenient to both faculty and evaluators and has generated very positive outcomes. In conclusion, a new faculty evaluation system has been developed. It provides constructive feedback to faculty members and serves as a more objective and transparent basis for making merit raise and award decisions. In addition, it can be readily adapted to evolving goals and needs of a department as well as different needs and cultures of different departments.