The development of buildings in the future will tend to the direction of green buildings. At present, most of the calculations of their costs usually use empirical models, which lack the basis for quantitative prediction. For the purpose of improving the accuracy of budget and control of project cost for green buildings, this paper applies interactive virtual reality (VR) genetic algorithm and analyze project budget accordingly. The prediction accuracy is effectively increased based on the mathematical analysis model. Finally, the test results suggest that the proposed algorithm can effectively improve the cost control efficiency and engineering quality of green buildings and reduce the construction cost of buildings.