Abstract Agriphotovoltaic (APV) systems emerge as a progressive solution to the dual challenge of sustainable energy generation and agricultural production. The thermal environment introduced by the photovoltaic (PV) panels plays a pivotal role within APV systems, influencing both plant growth and solar efficiency. However, a comprehensive investigation into the study for the regulatory effect of APV systems with different panel heights on the thermal environment has yet to be fully conducted. This study addressed this gap by carrying out test monitoring and establishing a thermal model based on computational fluid dynamics to explore the regulatory effect of different panel heights on air and soil temperature. Three panel heights of APV systems were selected, which were 2.5 m (H2.5), 3.2 m (H3.2), and 3.9 m (H3.9), respectively. The experimental plot for each panel height was segmented into 3 areas along the span direction, which were the southern, middle, and northern area. The key findings of this study revealed that the height of PV panels significantly affects the distribution of soil temperatures within the APV systems. At a reduced height of 2.5 m, the soil temperature in the middle area was notably higher compared to the northern and southern areas. When the panel height was increased to 3.9 m, soil temperatures in the northern and southern areas rose, while those in the middle area decreased. These results emphasize the pronounced sensitivity of soil temperatures to variations in panel height. Additionally, although air temperature differences across the varying panel heights were minimal, raising the panel height facilitated improved air circulation in the middle area. This enhanced airflow contributed to a more balanced heat exchange, thereby creating a more favorable environment for crop growth. In conclusion, adjusting the height of PV panels enables effective regulation of soil and air temperatures across different areas, thereby creating a favorable microclimate for crop growth. This study plays a crucial role in boosting the overall efficiency of APV systems, maximizing crop yields, and extending the return on investment period for the project.