Background: Despite previous studies reporting spatial in equality in diabetes prevalence across China, potential geographic variations in diabetes mortality have not been explored. Methods: Age and gender stratified annual diabetes mortality counts for 161 counties were extracted from the China Mortality Surveillance System and interrogated using multilevel negative binomial regression. Random slopes were used to investigate spatiotemporal variation and the proportion of variance explained was used to assess the relative importance of geographical region, urbanization, mean temperature, local diabetes prevalence, behavioral risk factors and relevant biomarkers. Results: Diabetes mortality tended to reduce between 2006 and 2012, though there appeared to be an increase in diabetes mortality in urban (age standardized rate (ASR) 2006-2012: 10.5-13.6) and rural (ASR 10.8-13.0) areas in the Southwest region. A Median Rate Ratio of 1.47, slope variance of 0.006 (SE 0.001) and covariance of 0.268 (SE 0.007) indicated spatiotemporal variation. Fully adjusted models accounted for 37 % of this geographical variation, with diabetes mortality higher in the Northwest (RR 2.55, 95 % CI 1.74, 3.73) and Northeast (RR 2.68, 95 % CI 1.70, 4.21) compared with the South. Diabetes mortality was higher in urbanized areas (RR tertile 3 versus tertile 1 ('RRt3vs1') 1.39, 95 % CI 1.17, 1.66), with higher mean body mass index (RRt3vs1 1.46, 95 % CI 1.18, 1.80) and with higher average temperatures (RR 1.05 95 % CI 1.03, 1.08). Diabetes mortality was lower where consumption of alcohol was excessive (RRt3vs1 0.84, 95 % CI 0.72, 0.99). No association was observed with smoking, overconsumption of red meat, high mean sedentary time, systolic blood pressure, cholesterol, and diabetes prevalence. Conclusions: Declines in diabetes mortality between 2006 and 2012 have been unequally distributed across China, which may imply differentials in diagnosis, management, and the provision of services that warrant further investigation.