Social and economic impact of change in the subsidies payment policy have been concern in past recent years. In this paper, a Computable General Equilibrium model is used to analyze the impact of change in subsidies payment system from indirect to direct state, on the price and quantity variables of domestic production and employment level economic sectors in two scenarios. The basic data are used in the framework of SAM year 2001. CGE model establishes the relations between accounts of SAM into a set of simultaneous nonlinear equations, by using the modern general equilibrium theory. In first scenario, indirect subsidy of manufacturing and services sectors is remove and its full payment in cash to the urban and rural households. In second scenarios, indirect subsidy of manufacturing and services sectors is remove and its direct payment to the proportions of 50. 30 and 20 percent to the households, economic sectors and Government respectively. The results show that by change in subsidy payment, composition of production and employment in economic sectors are change. The greatest decrease in domestic production and employment level and also the highest increase in the prices level is observed in the transport products. The mining sector is only sector that is face with positive production growth rate in both scenarios, and for most sector, a decline is forecast. But GDP level is face with decline to equal 2.78 percent respectively in first scenario and 3.05 percent in second scenario. In the end, with comparing two scenarios show that more the direct subsidies paid to households increase, more the domestic production of  some sector growth.