Chinese windmill palms (Trachycarpus fortunei) are widely planted in karst bedrock outcrop areas in southwest China because of their high economic and ecological values. The aims of this study were to investigate the foraging ability of Chinese windmill palm seedlings planted in six different types of karst microhabitat and to identify the main environmental factors that influence root foraging ability. We planted three-year-old Chinese windmill palm seedlings in six typical karst microhabitats (i.e., rocky trough, rocky surface, rocky gully, rocky soil surface, rocky pit, and soil surface microhabitats). One year after transplanting, the seedlings were excavated to determine the morphological parameters values of new roots and the nutrient concentrations of new roots and leaves. The root foraging ability of Chinese windmill palm seedlings, defined as new root length and new root surface area, was significantly greater in the rocky trough, rocky soil surface, and soil surface microhabitats than in the rocky gully, rocky surface, and rocky pit microhabitats (p < 0.05). Redundancy analysis revealed that the main positive factor affecting the rooting ability of Chinese windmill palm seedlings was soil thickness. Chinese windmill palm seedlings improved their root absorption efficiency by increasing their root length and root surface area under soil nutrient deficiency conditions. The organic carbon, total nitrogen, and available potassium in soil positively influenced the concentration of N and K in roots. Total potassium in soil negatively influenced the biomass of new annual leaves and concentrations of N, P and K in new annual roots and leaves. Chinese windmill palm seedlings can be grown in the different karst microhabitats, especially in the rocky trough, rocky soil surface, and soil surface microhabitats, and, therefore, it is suitable for use in the regeneration of karst forests.