In the present study, the variation patterns of leaf shape in different populations of individual Semiliquidambar cathayensis plants were analyzed to investigate the relationship among leaf shape variation, photosynthetic properties, and active compounds to understand the genetic characteristics of S. cathayensis and screen elite germplasms. The leaf shape of 18 offspring from three natural S. cathayensis populations was analyzed to investigate the level of diversity and variation patterns of leaf shape. Furthermore, photosynthetic pigment content, physiological parameters of photosynthesis, and the active compounds in leaves of different shapes were determined. Statistical analysis showed that the leaf shape variation in S. cathayensis indicated a high level of genetic diversity among and within the populations. Cluster analysis showed that the three natural populations formed two clusters, one whose offspring was dominated by entire leaves and another characterized by palmately trifoliate leaves. The differences in photosynthetic characteristics and active compounds of leaves of three different shapes were comprehensively evaluated using principal component analysis. Two principal components with a cumulative contribution rate of 92.768% were extracted, of which the highest comprehensive score was for asymmetrically lobed leaves. The leaf shape in different S. cathayensis germplasms exhibited distinct patterns, and there were some correlations between the photosynthetic properties and active compounds in leaves of different shapes. Thus, the leaf shape can be used to predict active compound content, and in turn, select varieties based on that purpose; it also provides a simple and effective method to classify S. cathayensis germplasms.