The photovoltaic conversion efficiency of commercial PV cells typically ranges between 20 and 30%, with residual energy accumulating as thermal energy within the photovoltaic modules. This study investigates waste heat recovery from operating PV cells through a fishery-photovoltaic complementary system, employing photovoltaic-thermal (PV/T) technology to transfer captured thermal energy to aquaculture water bodies. Our research specifically focuses on optimizing the heat transfer mechanisms to aquatic environments. Using finite element analysis (FEA), we developed a thermal regulation model for aquaculture ponds utilizing PV waste heat. The simulation evaluated three critical parameters: temporal variation, pipe diameter (5–45 mm), and initial water temperature (10–25 °C). Experimental results demonstrate that after 24-h operation, the pond temperature increased from an initial 15.304 °C to a maximum of 16.058 °C. Extended operation over 600 h (25 days) achieved sustained thermal elevation, with peak temperatures reaching 18.5 °C and minimum temperatures maintaining 17.7 °C, representing a 2.3–3.2 °C increase relative to baseline conditions. These findings provide critical thermal management data for designing optimized fishery-photovoltaic symbiotic systems.