Proton exchange membrane fuel cell (PEMFC) employing ammonia fuel present a prospective alternative for the operational dynamics of hydrogen fuel cells. Fuel cell systems based on hydrogen production from ammonia decomposition offer several advantages, including low-cost storage and transportation, high safety, high efficiency with low fuel cost, and importantly, are environmentally friendly with no carbon emissions during use. By regulating the hydrogen production from ammonia decomposition and the coordinated control of the PEMFC and energy storage devices, efficient and stable power generation can be achieved. In this study, with the electrical demand of 285 households in a community as the target output, an integrated system comprising an ammonia decomposer, membrane separator and PEMFCs is proposed. The effects of integrating different energy storage devices, including hydrogen tanks and lithium batteries, along with various ammonia decomposition input modes such as hourly, stepped, and constant flow strategies on the system's operation characteristics were systematically analyzed. Furthermore, the overall system performance and economic assessment were conducted, considering the equipment invested and the revenue generated for each strategic approach. It is demonstrated that the regulation strategy with constant flow input exhibited an average system efficiency of 52.49%, outperforming the stepped flow mode-based strategy, and the strategies based on the energy storage of lithium battery operate more stable than the ones based on hydrogen storage tanks. Overall, the strategy with constant flow, lithium battery stands out based on cost-effectiveness analysis.