As digital economy has dramatically evolved, new intellectual property rights protection has emerged as a pivotal issue which companies need to actively restxnid to. At the new digital era, the possession of new intellectual property rights determines the company values, and thus the protection of new intellectual property rights is getting more importance in the dimension of global competitiveness. The paper analyzes the changing aspect of digital economy and e-commerce paradigm, and explores the protection plan of new intellectual property rights focusing on e-commerce and digital goods transaction so that it can help the companies to strengthen their global competitiveness. After various case studies, we can find out that even though the companies have difficulty in settling out the strategies and policy due to the radical change of cycle in internet-centered digital economy, companies need to establish the systemic strategic plan to protect the new intellectual property rights stage by stage. Also, appropriate legal, institutional basis to protect the new intellectual property rights should be rearranged. The unsloved problems which relates with the protection of new intellectual property rights will be left for next research project.