Renewable energy based stand-alone microgrids are highly promising to supply electricity to isolated communities and remote locations. However, both buffer and long-term energy storage are essential due to the highly intermittent nature of renewable sources. By employing hydrogen energy storage with fuel cell and electrolyser in these microgrids, multiple outputs such as electricity, heat, water, and fuel, can be achieved. Design, development and optimization of efficient energy storage system remain a key challenge for the stand-alone microgrid technology. One must ensure that the microgrid satisfies the required electric load but is not over-designed, which is achieved by limiting the two performance parameters i.e., unmet electrical load fraction and excess electricity fraction. The capacities of wind turbine, electrolyser and hydrogen storage are optimized corresponding to the limiting values of unmet electrical load (fUL) and excess electricity (fEX) below 10 %. For the location of Ladakh which has rich availability of wind resource, the optimum size of microgrid is observed to be smallest as WT-20 kW, El-20 kW, H2-15 kg with fUL and fEX as 6.4 % and 8.9 % respectively. The Levelised Cost of Energy (LCOE) is also minimum as 0.89 $/kWh for the location of Ladakh. The distribution of wind resource has significant impact on the size of hydrogen storage. Uniform wind energy with higher velocity round the year reduces the capacity of hydrogen energy storage. Kanyakumari has non-uniform wind resource across different months of the year corresponding to which the capacity of H2 storage is as high as 370 kg.