The convective heat transfer coefficient (CHTC) at photovoltaic (PV) panel surfaces are critical for predicting its power output performance. However, the air flow condition and CHTC present discrepancy at different regional spaces of PV arrays due to wind- shielding effect. Existing studies often assume uniform coefficient for the thermal performance calculations, leading to an inaccuracies in PV array power generation prediction. In this paper, a three-dimensional numerical heat transfer model is established for PV array-roof system, and the effects of layout parameters of PV array on CHTC are systematically analyzed. The results demonstrate that installing PV array reduces partial CHTC on the roof, and significantly cause differences in heat exchange characteristics between first-row and rear-row PV panels. While the effect of PV panel’ size and PV array row space on CHTC are minimal. When the tilt angle of PV panel increase, the CHTC between roof and first-row PV panel (hpvr1) and CHTC between air and roof (hra) rose by 55.72% and 19.94%, respectively, while the CHTC between air and rear-row PV panels (hpva2) reduced. When the installation height of PV panel increase, the hpva1 doubled and hpva2 rose by 18.97%, whereas heat exchange between the roof and PV panels (hrpv) is attenuated. Increasing the array setback distance significantly affected the CHTC of the first-row PV panel, resulting in hpva1 decreased by 25.04% while hra increased by 19.80%. This paper reveals fundamental mechanisms governing CHTC at PV array surface, providing the basis for optimizing power generation efficiency and system layouts.