Based on Miami model, this paper calculated the human appropriation of net primary production (HANPP) in the middle reach of Heihe River basin, discussed the relations between the HANPP and ecosystem diversity, and compared the values of HANPP and ecological footprint (EF) in sustainability assessment. The results showed that the increase of HANPP decreased the ecosystem diversity, and the current average HANPP in study area was 38.61%. The HANPP in Suzhou and Ganzhou districts already exceeded the potential maximum productivity. Considering the climate change and the development of social-economics, the ecosystems in study area would face more stress in the coming 40 years. Comparing with EF, HANPP was more available for the assessment of sustainability in the sight of ecosystem function change.