Chili pepper (Capsicum annuum) is an important vegetable and condiment, but the current cropping pattern makes its continuous cropping obstacles increasingly prominent. Most studies show that reasonable rotation is an effective method and means to solve the continuous cropping obstacles of chili pepper. Industrial hemp (Cannabis sativa) is an ideal rotation plant, but the effect of industrial hemp rotation on alleviating the continuous cropping obstacle of chili pepper is not clear. In order to explore the effect of industrial hemp-chili pepper rotation on the growth and physiology of chili pepper, this study took the industrial hemp variety Yunma 1 and two local chili pepper varieties Taiyanghong and Yangjiaola as the materials in the agronomic experiment greenhouse of Yunnan University from 2018 to 2019. Pot experiments were carried out on chili pepper continuous cropping and industrial hemp-chili pepper rotation, respectively. The morphological growth and physiological and biochemical indexes of chili pepper after industrial hemp rotation were comparatively analyzed, and the effect of industrial hemp rotation on the growth and physiology of chili pepper in the later season was preliminarily explored. The results showed that the main physiological and biochemical indexes of chili pepper in the rotation group and the continuous cropping group had the same trend. However, compared with the chili pepper continuous cropping, the chlorophyll content of the two chili pepper varieties increased to a certain extent at 40, 50, 60 and 100 days after seedling thinning, while the activities of antioxidant enzymes (SOD and POD) and root activity also increased correspondingly, especially in the harvest period (100 days after seedling thinning) in the industrial hemp-chili pepper rotation. After the industrial hemp rotation, the net photosynthetic rate (P_n), stomatal conductance (G_s), intercellular CO₂ concentration (C_i) and transpiration rate (T_r) of the leaves of the two pepper varieties were significantly increased at 40, 50 and 60 days after seedling thinning, resulting in a significant increase in plant height, stem diameter, shoot dry weight and root shoot ratio at harvest stage. Compared with the chili pepper continuous cropping, the plant height of Yangjiaola and Taiyanghong increased by 20.65% and 16.85%, the stem diameter increased by 16.32% and 19.94%, the aboveground dry weight increased by 15.39% and 27.50%, and the root shoot ratio increased by 33.26% and 25.47% in the industrial hemp-chili pepper rotation, respectively. In conclusion, the industrial hemp rotation enhanced the physiological activity of late season chili pepper and better maintained the normal growth and development of chili pepper. The results have a guiding significance for the selection of reasonable planting mode of chili pepper in the future.