This paper is aimed at analyzing the recent issues concerning the negative effects of the implementation of integrated supervision and school institutional evaluation initiated by the Department of Education and local government. Using the survey results of "Education, Parenting and Family Lifestyle" and the "Post-Educational Reform Investigation" as evidences, this paper firstly addressed that the practices of evaluation programs has generated a series of problems, which have bad influences on schools evaluated. Secondly, this paper discussed some major issues which are highly connected with the school evaluation system, and listed some important drawbacks found within the process of evaluation. To conclude this paper, some practical suggestions are proposed to improve the quality of school evaluation system.