The hydrogen energy industry, as one of the most important directions for future energy transformation, can promote the sustainable development of the global economy and of society. China has raised the development of hydrogen energy to a strategic position. Based on the patent data in the past two decades, this study investigates the collaborative innovation relationships in China’s hydrogen energy field using complex network theory. Firstly, patent data filed between 2003 and 2023 are analyzed and compared in terms of time, geography, and institutional and technological dimensions. Subsequently, a patent collaborative innovation network is constructed to explore the fundamental characteristics and evolutionary patterns over five stages. Furthermore, centrality measures and community detection algorithms are utilized to identify core entities and innovation alliances within the network, which reveal that China’s hydrogen energy industry is drifting toward alliance innovation. The study results show the following: (1) the network has grown rapidly in size and scope over the last two decades and evolved from the initial stage to the multi-center stage, before forming innovation alliances; (2) core innovative entities are important supports and bridges for China’s hydrogen energy industry, and control most resources and maintain the robustness of the whole network; (3) innovation alliances reveal the closeness of the collaborative relationships between innovative entities and the potential landscape of China’s hydrogen energy industry; and (4) most of the innovation alliances cooperate only on a narrow range of technologies, which may hinder the overall sustainable growth of the hydrogen energy industry. Thereafter, some suggestions are put forward from the perspective of an industrial chain and innovation chain, which may provide a theoretical reference for collaborative innovation and the future development and planning in the field of hydrogen energy in China.