To address the uncertainty in hydrogen demand, this study develops a chance-constrained stochastic multi-objective optimization model covering the entire green hydrogen supply chain—production, transmission, storage, and utilization—aiming to minimize total system cost and maximize renewable energy consumption. The model optimizes the spatial layout, technology selection, and evolution pathways of provincial hydrogen production, transmission, and storage in China for 2022–2040. Results indicate that, under a compromise decision preference with a 99% confidence level, China’s green hydrogen production reaches 41.94 million tons by 2040, with 58.8% produced by alkaline electrolysis (ALK). Hydrogen transmission increases from 22,400 tons in 2022 to 1.26 million tons, with 80.1% transported via liquid hydrogen tank trucks and pure hydrogen pipelines. Hydrogen storage expands from 10,300 tons to 56.35 million tons, with the annual growth rate exceeding 461.6% from 2038 onward. Spatially, Inner Mongolia emerges as the largest hydrogen-producing province (20.3%), Anhui and Fujian as major hydrogen storage hubs (21.1% and 17.3%), northeastern and northwestern provinces as key exporters (56.9%), and central China as the main recipient region (36.7%). Increasing the confidence level significantly raises both total costs and water consumption, peaking at CNY 12.07 trillion and 476 million m3, respectively. Therefore, China should promote region-specific large-scale green hydrogen deployment by expanding proton exchange membrane (PEM) and solid oxide electrolysis cell (SOEC) production capacity, establishing hydrogen production hubs in Shanxi, Inner Mongolia, Shandong, and Anhui, strengthening transmission corridors in the northeast and northwest, and developing storage facilities in Qinghai, Ningxia, and Shanxi to foster an integrated green hydrogen supply chain.