In this paper, the effects of uncertain factors on the project scheduling with multi-factor disruptions problems is analyzed, considering the effects of customer satisfaction, cost and available resource. Its objective is to make reasonable disturbance recovery strategy and minimize disturbance in the project scheduling under the limit of resource constraints and project duration. The model of multi-project scheduling model with multi-disturbances is established, and the dual-population genetic algorithm is designed to solve this problem. Through the analysis, it is found that for multi-project scheduling problem with interferences, using local heavy scheduling scheme can conform to the actual needs of the project, and can more quickly making plan to restore the interference events affect scheduling system.