Urban biodiversity management is essential to realizing “Harmony with Nature” by 2050, and China has made significant progress but still needs to take more robust management measures. The Japanese urban biodiversity governance measures are systematically analyzed. Their governance tools are explained from three aspects: legal tools, indicator tools, and planning tools, and their participation forces are analyzed from three aspects: governmental forces, corporate forces, and public forces, and the specific practices at the city level are analyzed with Itami City as an example. The current status of urban biodiversity governance in China in terms of governance tools and participatory forces is summarized, and a comparison between China and Japan is made to highlight the current shortcomings. Five insights and recommendations for urban biodiversity governance in China are proposed: strengthening the legal system, rationalizing the management system and mechanism, forming an assessment and comparison mechanism, improving the planning and transmission mechanism, and building a public participation mechanism. The research results will help to formulate and implement more scientific policies and measures for urban biodiversity governance and achieve efficient governance.