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Abstract Global climate change, expected to be one of the most severe challenges that human beings have ever encountered, has had far-reaching impacts on ecosystems and humans, among which the potentially increasing chance of violent conflict has raised attention recently. However, several years of research have produced no consensus regarding whether climate variability affects the risk of armed conflict and how it may affect conflict. In this study, we built a geographically disaggregated method to explore the relationship between climate variability from normal climate conditions and armed conflicts both on a local and regional scale. With the 10,993 conflict records acquired in 25 African countries over 16 years from 2000 to 2015, we estimated the effects of temperature and wet day variability on conflicts in agricultural and non-agricultural areas, respectively, on gridded 1° resolution. The results showed that deviations from the normal climate have a systematical impact on the risk of conflict: The risk of violence rises with increasing deviations from the temperature norms in both non-agricultural and agricultural areas. Regarding the rainfall variability, in non-agricultural areas, the risk of violence grows with increasing anomalous wet days, either more or fewer days than the annual average, while in agricultural areas, increases in violence risk only exhibit under the impact of fewer wet days than the annual average. We expect these findings would provide empirical support for policymakers and relevant organizations who need to prepare additional law enforcement and/or peacekeeping resources when climatic anomalies are detected.