Researchers and scholars of management and behavioral sciences have tried to determine effective factors, which influence on efficiency and effectiveness in order to increase organization performance and they have tried to identify factors, which create job stress. In this research, we investigate the effect of job stress on job performance through emotional, organizational and moral intelligence. The study is a descriptive-analytic one, which is based on correlation, uses survey method to gather data and they are analyzed using structural equation modeling. The population of this research includes all the personnel of Registry Organization in Arak city. The results suggest that job stress influences on job performance through organizational intelligence and moral intelligence, but job stress does not influence on job performance through emotional intelligence. Regarding research hypotheses, results and findings after analyzing obtained data suggest that job stress influences on emotional, organizational and moral intelligence, but job stress does not influence on job performance. In addition, the results show that organizational and moral intelligence influence on job performance but emotional intelligence does not influence on job performance.