Photovoltaic (PV) power generation systems are increasingly installed on the factory rooftop. The installed PV power generation system exits a two-dimensional structure since the factories are usually designed to be square or rectangular. Motivated by real industry practice, this research proposes a two-dimensional performance sharing reliability model for the factory rooftop PV power generation system, where a common bus exists in each row and across all rows. The component availability is affected by both internal failure and external impacts. The system reliability is the probability that each component can meet its own demand and each row can meet its required demand after performance sharing. To mitigate external impacts, the factory rooftop PV power generation system employs both overarching protection and individual protection measures. We extend the universal generating function (UGF) technique to propose a reliability evaluation algorithm and use the genetic algorithm (GA) to determine optimal protection resource allocation to improve system reliability. Further, the proposed two-dimensional performance sharing reliability model is extended to consider multiple phased-mission. Numerical studies indicate that both expanding common bus capacity and optimizing the protection allocation strategy are effective ways to improve the factory rooftop PV power generation system reliability.