This paper sets up a multiindex department integration decision model with time feature based on synergetics theory.And the synergetic measurement decision matrix between department and government system can be calculated from the standardized treatment of the benefit and cost index.The leastsquares method multiindex optimized model was set up based on the weight vectors of each index and each time slots and the closedegree of each integration proposal to the positivenegative ideal proposal.According to the research this decision model can offer theory support for the optimal synergetic government system department integration decision and improve the synergetic degree of government system.