Abstract: The establishment of compliance mechanisms at the international level becomes the focus of stakeholders after the adoption of the Nagoya Protocol. The user and provider countries raise the elements and options on compliance mechanisms of the Nagoya Protocol according to the countries’ positions. Current negotiation processes indicate the differences on key issues of objectives, nature, compliance body settings, and the measures to promote compliance and address cases of non-compliance. This article analyzes options for core elements of compliance mechanisms raised by the user and provider countries, including whether mechanisms will be binding, common but differentiated principle will be stressed, a standing compliance committee with a strong monitor and review function will be established, and punitive measures for non-compliance will be established. Negotiation prospects point out that the mandatory nature of the compliance mechanism will be the core issue of the next round of negotiations. However, the settlement of disputes is ultimately dependent on the domestic legislation of parties. Finally, we provide three proposed countermeasures as follows: (1) elaborating special laws of genetic resources and improving relevant legal systems; (2) clarifying the supervising role in the scope of genetic resources and block the loss of genetic resource channels; and (3) regulating the utilization activities of other countries’ genetic resources.