Rural building clusters have significant prospects for solar energy application. However, the unclear impact of building shading on solar radiation distribution impedes their effective utilization. To address this issue, we conducted case studies in three villages with diverse morphologies in Nanjing. Employing a 12.5 m resolution digital elevation model (DEM), 3D building models, and hourly radiation simulation, we investigated the annual accumulated solar irradiance of these villages with and without building shading. The results showed that the impact of mutual shading is more substantial on facades than on rooftops. Without the shading, the façade annual accumulated solar radiation is 29.8–55.5% higher. While for rooftops, this ratio is only 2.9–4.7%. For different oriented surfaces, west-facing rooftops and facades are the most sensitive. Neglecting building shading leads to overestimations of 4.0–20.8% and 37.0–84.8% for the solar irradiance on them, respectively. Furthermore, the morphological disparity of villages would interfere with the impact of building shading. This study contributes to a more accurate assessment of solar energy potential in rural areas, which is vital for constructing a sustainable society.