In this study, mulberry branch from 12 planting areas in China were collected, and the contents of 12 compositions in these mulberry branch and their differences in bioactivities were compared. The effects of climate characteristics (environmental factors) in the planting areas on the compositions and the bioactivities of mulberry branch were analyzed by partial least square regression and multiple factor analysis. We found that the precipitation and temperature difference in the planting areas were important influencing factors, which could change the content and ratio of key compositions in mulberry branch, which in turn lead to differences in bioactivities. Planting environments with smaller temperature difference will make the anti-apoptotic effect of mulberry branch more prominent, and adequate irrigation will promote anti-oxidative effect of mulberry branch. These research results provide evidence for improving mulberry planting conditions and rational use of resources from the perspective of mathematical analysis.