This paper examines the relationship between compensation and reward system for employees and employee performance evaluation system with human resources strategies and business strategy of Islamic Republic of Iran Customs Administration (IRICA). The statistical population of this research included the directors, deputies for financial affairs and experts of human resources of customs administration, among whom 285 participants were selected as statistical sample. This is a descriptive-analytical study. Regression and correlation tests were used to test the hypotheses. According to the results, the obtained first hypothesis of the research was confirmed. Therefore, business strategies have a positive and direct impact on human resources strategies. The second and third hypotheses of the research were also confirmed. On the basis of this result, we can say that the strategies of human resource and business positively and directly influence the employee compensation system. The third and fourth hypotheses of research were confirmed as well; therefore, the business and human resources strategies positively and directly influence employee performance appraisal system. Furthermore, the research showed that, compared with the cost leadership strategy, the differentiation strategy has a stronger and more consistent relationship with the compensation system and the merit-based performance appraisal system.