The early Cenozoic sedimentary sequences in Yunnan not only recorded the early tectonic deformation process of the India-Eurasia collision,but also recorded regional climate and biological evolution,and have significant scientific research value. We carry out rock magnetic study of the Late Eocene Caijiachong-Xiaotun formations in the Qujing basin, Yunnan. Through magnetic susceptibility and sedimentary facies analyses,we establish four evolution stages in the Caijiachong-Xiaotun formations. The sedimentary environments evolved from river-shallow lake sedimentary facies to half deep lake sedimentary facies, accompanied by gradually reduced magnetic susceptibility values in the first three stages. Abrupt magnetic susceptibility values increase in the fourth stage,with the presence of pyroclastic material. Combined with other evidences, rock magnetic analyses of representative samples indicate that the reduce of magnetic susceptibility values was likely caused by pedogenesis weakening process that leading to the change of magnetic mineral type and content. Rather than a pedogenesis weakening process by dry and cold climate,the low magnetic susceptibility values were likely caused by a gradually transformation process from oxidation environment to a reduction environment,which was a result of changing sedimentary environment from river-shallow lake sedimentary facies to half deep lake sedimentary facies. Climate change and /or local tectonic activities might be the causes of the sedimentary environment change. Our study suggest that, the change of susceptibility value in certain degree responds to paleoclimate change in a unit source environment, and hence susceptibility can be used as an effective proxy in Early Cenozoic paleoclimate study.