Morality cultivation is a fundamental task for university. Performance appraisal system is an important link and method to improve work efficiency. Based on the innovative management practice of college student affairs, this paper, with the guidance of morality cultivation, discusses the practical significance of constructing a performance appraisal system for college-level student affairs in university. Taking target management as the main line, introducing the performance appraisal mechanism model of student affairs in college-level, from the target setting and decomposition, process management, summary evaluation to performance optimization and improvement, a set of control system framework and implementation path for college-level student work are established. Finally, using the key performance method, the paper preliminarily constructs the performance appraisal index for faculty-level student affairs in colleges and universities, and uses the analytic hierarchy process to quantify the appraisal index, which makes it more scientific and reasonable.