Previous studies on patterns in ungulate size variations have emphasized the effect of a particular environmental factor. However, multiple environmental factors may influence the body size. In this study, we used several skull and limb measurements to examine size variations among island populations of sika deer in southern Japan considering the effects of multiple environmental factors. All measurements differed between populations. Condylobasal length (CBL) and metacarpal length (ML) that had large variations among populations were affected by common environmental factors (island area and precipitation). Since these factors reflect the availability of food resources, the causal factor of body size variation may be food resources. Interpopulation variation in ML was greater than that of CBL, indicating that ML may be affected by additional factors besides the common factors shared with CBL. Specific environmental factors of relative ML were precipitation and slope. A common direct cause of those environmental factors was discussed in relation to topography. Analyses of phenotypic variation using multiple measurements with multiple environmental factors are useful to gain insight into underlying causes and can lead to identification of a measurement-specific variation with a specific driving force.