Countries such as China are facing a bottleneck in paths to carbon neutrality: abating emissions in heavy industries and heavy-duty transport. There are few in-depth studies of the prospective role for clean (green/blue) hydrogen in these “hard-to-abate” (HTA) sectors. Are current mitigation technologies in HTA sectors effective? What are the roles for clean hydrogen towards carbon neutrality? We carry out an integrated modeling analysis to answer these questions. Results show that, first, clean hydrogen as both energy carrier and feedstock can significantly reduce heavy industry emissions. Second, clean hydrogen can fuel up to 50% of China’s heavy-duty truck and bus fleets by 2060 together with significant shares of shipping. As a side benefit, a realistic hydrogen scenario, reaching 65.7 Mt of production in 2060, could avoid $1.72 trillion new investment cost compared to a no-hydrogen scenario. This study provides strong evidence for countries facing challenges similar to China in addressing requirements to reduce emissions from their recalcitrant HTA sectors towards carbon neutrality.