The photovoltaic power generation system is a kind of clean, safe, convenient and efficient power generation industry. In recent years, as one of water photovoltaic power generation systems, the “fishingphotovoltaic complementation” has a significant development, which solves the problem of the scarce traditional photovoltaic power station construction land resources and improves the efficiency of the comprehensive land utilization. In order to prevent and reduce the equipment damage and personal injury of the water photovoltaic power generation system caused by lightning to ensure the safe and reliable operation of the photovoltaic power generation systems, by analyzing the lightning environmental characteristics and its damage where the project is located, combining with the layout form and structure characteristics of the water photovoltaic power generation systems, a comprehensive lightning protection scheme is put forward, which uses an external lightning protection system composed of the airtermination system, downconductor system, and earthtermination system to prevent the direct lightning flash damage, and comprehensively uses the equipotential bonding and common earthing system, electromagnetic shielding, and wiring reasonably, installing surge protective devices (SPDs), and so on to effectively reduce the damage of the electrical and electronic systems in the photovoltaic power generation systems caused by lightning overvoltages and lightning electromagnetic impulses.