Currently, there are few research on the influence of human reliability upon the reliability of integrated substation automation system (ISAS). This paper proposed a risk assessment method of ISAS considering human reliability. First, according to the operators work condition, estimate the human error probability based on analytic hierarchy process-smart substation automation system to correct the failure probability of physical devices. Then, adopt the function decomposition based method to assess the failure risk of functions. Finally, obtain the failure risk of ISAS by mixing the function risks to characterize the reliability of ISAS and offer guidance to dispatching department. The big impact of human reliability on the ISAS risk is demonstrated in case study, which means considering human reliability is more objective than the traditional method.