Protected areas play significant roles in protecting biodiversity by mitigating human activities. As an indicator for human activities, the human footprint (HF) can be used to assess the effectiveness of protected areas. We developed a HF dataset for the Sanjiangyuan region in China after localizing the global HF model. Then we used it to assess the effectiveness of Sanjiangyuan nature reserve (SNR) in mitigating human pressures. Our results suggest that the HF value for the Sanjiangyuan region was generally low from 1995 to 2015, with a fluctuating increasing trend. The SNR is partially effective in mitigating human pressures. For 2005–2010, the HF values decreased both within and outside the reserve with more decreases for the outside. For the three functional zones of the SNR, our results show that the HF values decreased during 2005–2010 for all of them, with the largest decrease in the experimental area, and increased during 2010–2015, with the lowest increase in the core areas. The results we obtained are consistent with ecological indicator-based assessments. It is a challenge for the government to balance conservation and development in establishing Sanjiangyuan National Park.