The hydrogen production rate and lifetime of photovoltaic (PV)-driven proton exchange membrane (PEM) water electrolysis systems are significantly related to the fluctuating input characteristics to the PEM, which is caused by the weather conditions and types of PV cells. However, most of the existing studies focus on the theoretical optimization under steady state conditions, and there is a lack of understanding on the matching characteristics of weather conditions and different PV-PEM systems. Therefore, this study selects the commercial PV panel based on monocrystalline silicon (mono-Si) and PV panel based on cadmium telluride (CdTe), and compares the dynamic hydrogen production performance of the two types of PV-PEM systems under different weather conditions, both experimentally and numerically. The experimental results show that under sunny weather conditions, the average daily power generation of the PV system based on CdTe is 5.06% higher than that of the PV system based on mono-Si, and the hydrogen production is increased by 4.79%. While with significant solar irradiation fluctuation, the output power fluctuation of PV panels based on CdTe is 15.74% lower than that of PV panels based on mono-Si. However, limited by the lower nominal efficiency of the PV panels based on CdTe, the solar-to-hydrogen (STH) efficiency of the CdTe PV-PEM system is 7.60–8.65%, which is lower than that of the PV system based on mono-Si (10.89–12.15%). To enhance hydrogen production and extend system lifespan, PV technology based on CdTe demonstrates greater advantages than PV technology based on mono-Si when coupled with PEM electrolyzers, particularly in regions where installation space is not a constraint.</p