With emphasis on finding storage solutions for renewable based power plants, hydrogen has emerged as one of the prominent options. Hydrogen required in fertilizer, oil and gas industries etc., is produced using fossil fuels which emits carbon dioxide 10 times the produced hydrogen. It is important to produce the hydrogen from green energy sources for this industrial use or for the energy storage use. Solar energy harvested from Photo-Voltaic (PV) technology can be used to produce hydrogen in an alkaline electrolyzer. Directly coupling the PV and electrolyzer systems will have least components contributing to inefficiencies, complexities etc. In this study, a tool was made using MATLAB-Simulink, to optimize the PV-Electrolyzer directly coupled system. In literature many authors have done the same but none of them have included variation in space irradiance over PV farm, variation in PV module parameters due to manufacturing defects or defects arising over the period of use. These variations affect the IV curve of PV modules and in turn affect the performance of the whole system. It was observed that after optimizing, the coupling efficiency in the range of 90-95% could be achieved in directly coupled systems with shorter string lengths of PV. This was even after including the variation up to 20% in parameters like irradiance and PV module parameters. If the best configuration is not available in the market, then the set of next best configurations is available as output of simulation. Even with variation of 10% in input parameters, the maximum difference between the global maximum and other local maximums in the results is 3%. This 3% compromise results in energy loss of 870 kWh and 148 euros loss per year for a 50 kWp system. Which is 2.96 Euros/kWp loss, at 1 GW scale it may result into a loss of 2.96 million Euros, if we ignore the variations. In comparison to the DC-AC-DC configuration that comprises of inverter, rectifier and transformer, the directly coupled system performed better. The efficiency was almost 5-10% more for directly coupled system in comparison to DC-AC-DC system. The weighted efficiency for both the configurations were calculated, where the weights were based on the occurrences and the energy contribution of an irradiance bracket. The weighted efficiency for directly coupled system was 95.7% and for DC-AC-DC was 90.63% for Amsterdam. Even after considering all the seasonal, weather parameter and module parameter variations, directly coupled PV-Electrolyzer systems with shorter string length and bigger electrolyzer cells gave the best efficiency amongst all, which was above 90%.