This research introduces the three variables of spillover effect, research and development efficiency, and cost of mergers and acquisitions as the chief factors affecting independent research and development and technology mergers and acquisitions based on a two-stage game theory model of research and development strategies. Using these three variables, this research explains the selection of independent research and development or technology mergers and acquisitions according to profit maximization. Based on the theory model, this research finds that costs of mergers and acquisitions and spillover effects play a significant role in research and development decisions. In addition, excessive costs of mergers and acquisitions can increase research and development expenditures, therefore reducing profit and affecting the organizational operation and development. Therefore, when the costs of mergers and acquisitions exceed a certain level, companies will abandon technology mergers and acquisitions and choose independent research and development; and a higher knowledge spillover effect reduces the costs of independent research and development, therefore increasing profit. In conclusion, given certain costs of mergers and acquisitions, a higher spillover effect helps business organizations to choose independent research and development strategies.