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 it is hard to incorporate the versatile contributions of individual faculty members. Here, we propose a quantitative and objective faculty performance evaluation method. We established a well-structured quantitative evaluation system which scores faculty performance in key activities using expectation-based formula on key measures and then incorporates personalized flexible weights to integrate them into three area scores in teaching, research, and service as well as an overall score. It was implemented in a programed excel form, making it convenient to both faculty and evaluators and has generated very positive outcomes such as higher faculty satisfactory and improved productivity as indicated by associated increases in publications and new research grants etc. In conclusion, the quantitative faculty evaluation system provides more objective and transparent annual evaluation and a 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.