The transition of energy system from fossil-based to low-carbon based is crucial for sustainable development. Hydrogen is a potential fuel of the future as it has a clean emission aside with high gravimetric energy density. To minimise the cost of the future hydrogen supply network, the location of hydrogen production site should be well-selected. While most of the past studies have employed mathematical model to optimise the hydrogen supply chain, spatial conditions such as availability of energy sources, transportation network and land-use should also be considered when identifying the optimal site location. This study proposes a two-stage spatially-explicit hydrogen supply chain optimisation framework that integrates the Geographical Information System and mathematical optimisation model. The first stage involves spatial analysis to identify potential production site and demand site locations based on the geographical factors. Transportation distance between the potential production sites and the demand sites will be computed and input to the mathematical optimisation model. In the second stage, the mathematical model is solved to identify the cost-optimal production site location. The proposed methodology is applied to Malaysia case study and the optimal site location has been identified. The annual cost of the optimised hydrogen supply chain is determined to be 159.3 million USD.