In this paper, we discuss the effects of intellectual property rights (IPRs) on FDI and indigenous innovation and the overall effects of IPR on the Southern and Northern countries. Our model predicts that tighter IPR is good for FDI and indigenous innovation; however, the effects vary according to the initial resource endowment such as skill level and absorptive capacity. By a game theory model, we also find that tighter IPR benefits both sides if the innovation is the common knowledge to both players, and it improves indigenous innovation and welfare in a short term, but they will emerge in the long run. We also discuss the further direction to an empirical study. Finally, we make the following conclusion: IPR is part of business environment, and tighter IPR in progress is good for boosting welfare of both sides. It is time to build a better environment for IPR, but the cost of patent enforcement policy and the trade barrier must be taken into account.