The protection scope of IPR is the primary policy tool for stimulating innovative enterprises to invest in R&D. It exerts an influence on the IPR transaction between transferor and transferee enterprises by affecting the acquisition cost and profitability of IPR. A multi-stage game model of two enterprises with asymmetrical abilities is built and general balanced analysis is conducted. Results show that expanding protection scope of IPR is able to raise enterprise income and stimulate enterprises to invest more on R&D only if the initial R&D investment reaches at a certain scale. Under the established R&D investment, expanding IPR protection scope margin would increase the cost of technology transfer, boosting profit for the transferor, meanwhile decreasing profit for the transferee and bringing the negative influence on social welfare. The negative side effect would be mitigated only after the distensible effect of R&D investment is achieved. Therefore, while expanding the protection scope of IPR, the auxiliary measures, such as preferential taxation policy for enterprise R&D investment and IPR trade promotion among enterprises, should also be introduced.