Preclinical imaging with photoacoustic tomography (PAT) has attracted wide attention in recent years since it is capable of providing molecular contrast with deep imaging depth. The automatic extraction and segmentation of the animal in PAT images is crucial for improving image analysis efficiency and enabling advanced image post-processing, such as light fluence (LF) correction for quantitative PAT imaging. Previous automatic segmentation methods are mostly two-dimensional approaches, which failed to conserve the 3-D surface continuity because the image slices were processed separately. This discontinuity problem further hampers LF correction, which, ideally, should be carried out in 3-D due to spatially diffused illumination. Here, to solve these problems, we propose a volumetric auto-segmentation method for small animal PAT imaging based on the 3-D optimal graph search (3-D GS) algorithm. The 3-D GS algorithm takes into account the relation among image slices by constructing a 3-D node-weighted directed graph, and thus ensures surface continuity. In view of the characteristics of PAT images, we improve the original 3-D GS algorithm on graph construction, solution guidance and cost assignment, such that the accuracy and smoothness of the segmented animal surface were guaranteed. We tested the performance of the proposed method by conducting in vivo nude mice imaging experiments with a commercial preclinical cross-sectional PAT system. The results showed that our method successfully retained the continuous global surface structure of the whole 3-D animal body, as well as smooth local subcutaneous tumor boundaries at different development stages. Moreover, based on the 3-D segmentation result, we were able to simulate volumetric LF distribution of the entire animal body and obtained LF corrected PAT images with enhanced structural visibility and uniform image intensity.