It is well acknowledged that high nitrate concentration would negatively affect the biological denitrification activity, especially in the presence of nitrite accumulation. In this study, a novel granular partial denitrification (PD) process was developed, and the impact of nitrate concentration (120−960 mg N/L) on PD granules was investigated by close monitoring of the operational performance, physicochemical characteristics, and microbial community. Results indicated that the effluent nitrite increased with the nitrate concentration, with a maximum value of 492.4 mg N/L obtained. And the maximum denitrification activity in situ was found not to be decreased despite high nitrite accumulation; it was maintained at 0.24 g N/g VSS/h, suggesting the high tolerance of PD granules to the nitrite. The granule size increased with the influent nitrate, and the compact PD granules, however, were observed to be disintegrated at 960 mg N/L of nitrate, which was likely attributed to the substrate diffusion limitation in larger granules, with the cavity formed in its inner part. In addition, microbial analysis revealed that bacterial richness and the diversity of PD granules were decreased, and Gracilibacteria that was supposed to be responsible for maintaining the PD granule structure was largely reduced at a high nitrate concentration, which was likely to be another major reason for the disintegration. This study revealed the potential causes for the disintegration of PD granules, which offer theoretical support and technical guidance to ensure the stability of PD granules in treating high nitrate wastes for efficient nitrite production.