Continuous cropping obstacles (CCO) refer to abnormal crop growth resulting from consecutive cultivation of related crops in the same soil. Panax notoginseng is severely affected by CCO. Crop rotation is the most effective approach to alleviate CCO. This study examined the impact of eight crop rotations on soil fertility, crop photosynthetic physiology, yield, and autotoxic substance levels in subsequent P. notoginseng crops. The findings indicate that maize is the most suitable rotational crop for P. notoginseng, significantly reducing saponin content by 18.5% and increasing biomass and chlorophyll content by 32.8% and 46.3%, respectively. Correlation analysis revealed that ginsenoside R1 enhances antioxidant enzyme activity, while saponin-like autotoxic substances are negatively correlated with chlorophyll. In conclusion, allelopathic autotoxicity primarily impairs plant growth by inhibiting photosynthesis and inducing changes in antioxidant system activity, leading to cell structure damage. Introducing maize in crop rotation reduces autotoxic substance levels and increases P. notoginseng biomass.