China (Shanghai) Pilot Free Trade Zone (referred to as "Shanghai FTZ") is not an international free trade area under the WTO regime, but a domestic special economic zone established by according to "China's WTO Accession Protocol". Intellectual property protection is an important issue closely followed by the WTO, intellectual property protection in the Shanghai FTZ is also an unavoidable focus. The Shanghai FTZ intends to be a real free trade zone, i.e., goods coming from and leaving for overseas will require no customs supervision. But Shanghai FTZ is not a safe haven for intellectual property infringement. Shanghai FTZ should strengthen intellectual property protection policy system, enforce of intellectual property customs protection strictly, and the use of "pilot" preferential policies, to provide a demonstration effect on national intellectual property policy system on the aspects of intellectual property rights management and enforcement institution, and to provide empirical support for international harmonization of intellectual property rules.