Camellia flavida, a golden Camellia with yellow petals, is a typical shade-tolerant shrub in karst regions. The aim of this study was to explore whether karst habitat heterogeneity contributes to the fine-scale spatial genetic structure (SGS), gene flow, and genetic differentiation of C. flavida at the small scale within a 15hm² plot of northern tropical karst seasonal rain forest in Nonggang, based on 13 microsatellites. The results indicated that there was a significant SGS in C. flavida within a distance of 50 m, the intensity of which is moderate (Sp = 0.0248) among shrub and gravity-dispersed species. The mean seed and pollen dispersal distances of C. flavida were short at 12.47 m and 29.03 m, respectively, with 72.2% of pollen and 81.0% of seed being mainly spread within 20 m. In addition, there was significant genetic differentiation among four populations at the small scale (distance between populations < 1 km), and even between two patches separated by a distance of only 100 m. It is concluded that karst habitat heterogeneity significantly influences the gene flow of C. flavida, leading to comparatively strong SGS and genetic differentiation at the small scale.