Desertification threatens food security and human nutrition through its impacts on agricultural productivity. The damage caused by desertification includes both direct, on-site impacts and wide-ranging indirect, off-site effects. In this study, we applied a multi-region input-output framework to estimate the direct and indirect consequences of desertification in China, and associated impacts on macronutrient intake. We found that desertification causes macronutrient loss and significant losses in employment, income, and value added throughout upstream supply chains. Our results indicate that desertification affected around 2.1 million jobs, resulted in income loss of about US$ 17.3 billion, and a loss in value added of about US$ 28.6 billion in year 2017. In terms of sub-national regions within China, macronutrient losses are highest in Inner Mongolia, with the population facing a 24% reduction in energy, 21% reduction in protein, 33% reduction in fat, and 26% in carbohydrates. The findings of our study suggest the importance of combating desertification, which is also indicated as a priority in the Sustainable Development Goal (SDG) 15 of the United Nations 2030 Agenda.