The hydrogen industry is of great significance for global energy system transition and decarbonization; thus, the holistic planning of hydrogen infrastructure from a supply chain level is necessary. To this end, first, the framework and methods in the hydrogen infrastructure deployment research were investigated systematically. Second, a hydrogen supply chain design (HSCD) model and a hydrogen refueling station location (HRSL) model were constructed. In view of the limitations of the two models, this paper reformulated the HRSL model through alternating the objective function and constraint, then proposed an integrated planning model using the & varepsilon; ${\epsilon}$-constraint method, which relaxed the assumption condition and expanded the decision-making boundary of the original model, realizing the reasonable equilibrium of multiple segments. Finally, a case study was conducted using the Yangtze River Delta region as an example, and the main findings were as follows: (1) To meet the hydrogen demand of 25494t/d, the Yangtze River Delta region needs to build 94 coal gasification hydrogen plants, storage facilities with capacity of 12747t, transmission modes with capacity of 2333t/d, and 150 hydrogen refueling stations. (2) Railways have more advantages in large capacity and long-distance hydrogen transmission. (3) Road segments with higher traffic flow often have a higher capture proportion. (4) The investment cost accounts for the majority of hydrogen production plant construction, which is 43.80%.