Abstract: Investigation and sampling of three populations of Citrus macroptera var. kerrii distributed in Xishuangbanna. The variance analysis, the correlation analysis and other methods were used to discuss the variation of 15 morphological characters of leaf and seed in the population and among the populations of Cmacroptera var. kerrii. The results showed that the variance degree of all traits in the same population were different, the difference of 9 traits among populations was very significant, that of one trait was significant, and that of other 4 traits were not significant, the morphology of seeds was more stable than that of leaves. the coefficients of variance of 15 traits were respectively as follows: the WWL (width of wing leaf) 2964%, the LWL (length of wing leaf) 2296%, the WL (width of leaflet) 2246%, the LL (length of leaflet) 2097%, the LWL/LL 2073%, the TLL (total length of leaf) 2009%, the LL/LWL 1747%, the WWL/WL 1697%, the LS/WS (length of seed/width of seed) 1497%, the LWL/WWL 1339%, the TS (thickness of seed) 1234%, the LL/WL 1204%, the WS 1137%, the LWL/TLL 1039%, the LS 1010%. Most correlation efficient of 11 leaf traits and 4 seed traits were obvious positive or negative.