Combined cooling, heating, and power (CCHP) systems, with high efficiency and low pollutant emissions, are ideal for addressing these issues. Proton exchange membrane fuel cells (PEMFCs) exhibit high energy conversion efficiency, good stability, and concurrent heat production, which makes them suitable for powering residential cooling and thermal supply systems. For a PEMFC integrated energy supply system, flexible loads can realize the “interaction” between the supply and demand sides by changing their own energy consumption time or load size. This study introduces three systems under flexible load regulation. A comprehensive evaluation explores flexible regulation impacts. The results indicated that with flexible regulation, the energy efficiency of most systems in summer was improved, the exergy efficiency and CO2 emission reduction rate of all systems increased, and the average daily cost decreased. This study further analyzed the changes in energy efficiency, exergy efficiency, environmental benefit, and economic benefit of each cogeneration system under variable loads and formed the design principle. The CCHPH-VCC (CCHP with humidity control and vapor compression cycle) system had the best overall performance in the studied cooling/power ratio range; however, the CCHP system can be selected at a cooling/power ratio less than 0.69 for summer operation if the focus of the system selection is on environmental and economic benefits.