To mitigate transient thermal shocks in lasers and reduce thermal stresses caused by temperature fluctuations, the use of phase change materials (PCMs) in thermal management systems is a viable solution. This study proposes an innovative two-dimensional transient heat transfer model specifically designed for plate-fin phase change heat exchangers (PFPCHEs). The model meticulously simulates the complex heat transfer phenomena within the heat exchanger, including fluid convection, solid thermal conduction, and the phase change processes of PCM. The convective heat transfer coefficient between fluid and plate is calculated using the Wieting correlation. An advanced pulse-mode experimental test platform was constructed to validate the model, dynamically monitoring and recording outlet temperatures and heat exchange performance for stringent experimental comparison. The research explores the impact of key operating parameters such as initial temperature, flow rate, and inlet temperature of the cooling cycle on the performance of the heat exchanger, providing valuable design and control strategies for transient thermal management of laser systems. The experimental results confirm that the model accurately predicts the dynamic response characteristics and temperature distribution of PFPCHEs under multi-cycle pulse loads, with 96% of the predictions within a 10% error margin. A significant finding is that the initial temperature has negligible influence on the heat transfer characteristics when it is below the solid phase temperature of the PCM. Moreover, by meticulously adjusting the flow rate and inlet temperature of cooling cycle, it is possible to effectively maintain the stability of the outlet temperature throughout the entire pulse cycle. This is crucial for minimizing temperature fluctuations within the thermal management system and extending the service life of electronic components.