Malaria is a climate-sensitive disease and different climatic conditions affect the propagation of malaria vectors thereby influencing malaria incidence. The present study was undertaken to delineate malaria distribution across different climate types and sub-types in India and assess its significance as a malariometric in the ongoing elimination activities. All Indian districts were classified into three major climatic zones (Tropical, Temperate, and others (Arid, Cold, and Polar) based on the Köppen-Geiger climate classification system. The Annual Parasite Incidence (API) of malaria was analyzed in these climatic zones using the Kruskal Wallis test, and a post hoc comparison was done using the rank-sum test with an adjusted p-value for the level of significance. Further logistic regression was used to investigate the association of these climatic zones with high malaria incidence (i.e., API>1). The majority of Indian districts fall in Temperate (N = 270/692 (39.0%)) and Tropical (N = 260/692 (37.6%)) regions, followed by Arid (N = 140/692 (20.2%)), Polar (N = 13/692 (1.9%)) and Cold (N = 9/692 (1.3%)) regions. Three climate zones: Arid, Polar, and Cold were similar in terms of malaria incidence over the years and thus were grouped into one. It was found that the tropical and temperate zones display a significantly higher burden of malaria as compared to others for the studied years (2016–2021). Future projections of climate suggest a significant expansion of tropical monsoon climate towards central and northern India, along with a growing footprint of tropical wet savannah climate in the northeast of India by 2100, which could increase the risk of malaria transmission in these regions. The heterogeneous climatic zones of India play an important role in malaria transmission and can be used as a malariometric for the stratification of districts destined for malaria elimination.