Abstract: Objective The leaf phenotypic traits of an endangered plant Tetracentron sinense were measured to understand the phenotypic variation. The purpose is to discuss the mechanism causing its endangering from the perspective of genetics and the ability to adapt to hostile conditions in order to provide some references for effective conservation and management. Method Seventeen leaf morphological characteristics and leaf epidermis micromorphological characteristics from 90 individuals of fourteen populations were measured. Nested analysis of variance, multi-comparison, principal components analysis, cluster analysis, and correlation analysis were used to study the leaf phenotypic variation and its relation to environmental factors. Result (1) Analysis of nested variance for all the traits showed significant differences among and within populations. (2) The mean phenotypic differentiation coefficient for all the traits was 46.69%, and the variation within populations (31.83%) was higher than that among populations (28.85%), indicating that the variance within population is the main source of the phenotypic variation of the species. (3) The range of variation of coefficient of variance among the 17 traits was 4.17%~26.25%, and the average was 12.56%. (4) The leaf phenotypic variation of T. Sinense was related to the environmental factors, such as mean annual sunshine duration, mean temperature in July, and mean annual precipitation. The gradient rule of leaf phenotypic characteristics is presented along with longitude, latitude and altitude. (5) According to the cluster analysis based on the results of principal components analysis, the 14 natural populations of T. sinense could be divided into three groups. Conclusion There were moderate level of phenotypic differentiation among populations and low level of phenotypic variation within populations. The decreasing distribution range and poorer adaptability to changing environment were the main factors influencing the survival of T. sinense. According to above conclusions, some corresponding conservation measures were proposed to protect natural populations of T. sinense.