Abstract: Integrating biodiversity conservation into territorial spatial planning is both a strategic requirement of the global conservation agenda and an intrinsic component of China’s ecological civilization agenda. Municipal and county-level territorial spatial master planning is the most important level at which biodiversity conservation is translated into spatial governance. This paper analyzes biodiversity conservation needs at the municipal and county level, develops a working framework for introducing and strengthening biodiversity conservation throughout the planning process, and proposes a technical pathway of “constructing a whole-territory conservation spatial network—defining hierarchical conservation-oriented spatial governance—proposing restoration measures for important habitats.” Taking Yunlong County, Yunnan Province, as a practical case, the paper explores specific application scenarios. It concludes that this technical pathway must be further improved through accumulated empirical evidence from multiple regions, and that future work should strengthen biodiversity monitoring and spatial database construction, unify planning technical standards, and promote coordinated management across ecological regions.