Abstract Biodiversity hotspots at the global and national scale have contributed important information for biodiversity conservation; however, in hotspot designation two kinds of “gap” greatly limit conservation planning, which this study identifies as the “scale gap” and the “conservation gap”. To address the gap, we integrated systematic conservation planning (SCP) with gap analysis to optimize solutions of protected areas planning at local scales. In this study, we presented a quantitative spatial methodology for prioritization and downscaled to a planning case study in the province of Shanxi, China. First, the spatial distribution of 54 threatened plant species were mapped at fine resolution, and scenarios of conservation targets for taxa were generated according to species attributes, which are both the necessary inputs in selection algorithm of priority conservation. Then we determined 17 priority conservation areas using SCP, which only cover ∼5% of the total area but could represent 100% of the threatened plant species in Shanxi Province. We confirmed that priority conservation areas determined based on SCP can achieve maximum efficiency of conservation, especially considering representation of small-ranged species. Further, through overlapping priority conservation areas with nature reserves, six conservation gaps were identified for future conservation efforts. Our findings provide suggestions for protected areas network planning of botanical conservation in real-world contexts. The proposed method of integrating SCP with gap analysis can be generally used in bridging the gap between biodiversity priority areas and protected areas in proactive planning and management protocol for biodiversity conservation.