Pericytes and glial cells are accessory cells of the neurovascular networks, which have been reported to participate in scar formation after tissue injury. However, it remains unclear whether similar reactive cellular responses occur in pancreatic intraepithelial neoplasia (PanIN). Here, we develop 3-dimensional (3-D) duct lesion histology to investigate PanIN and the associated pericyte, glial, and islet remodeling. Transparent mouse pancreata with Kras^G12D mutation were used to develop 3-D duct lesion histology. Deep-tissue, tile-scanning microscopy was performed to generate panoramic views of the diseased pancreas for global examination of the early-stage and advanced duct lesion formation. Fluorescence signals of the ductal and neurovascular networks were simultaneously detected to reveal the associated remodeling. Significantly, in the Kras^G12D-mutant mice, when the low-grade PanINs emerge, duct lesions appear as epithelial buds with peri-lesional pericyte and glial activation. When PanINs occur in large-scale (induced by cerulein injections to the mutant mice), the 3-D image data identifies: i) aggregation of PanINs in clusters in space, ii) overexpression of the pericyte marker NG2 in the PanIN microenvironment, and iii) epithelial ingrowth to islets, forming the PanIN-islet complexes. Particularly, the PanIN-islet complexes associate with the proliferating epithelial and stromal cells and receive substantial neurovascular supplies, making them landmarks in the atrophic lobe. Overall, the peri-lesional pericyte and glial activation and formation of PanIN-islet complex underline the cellular heterogeneity in the duct lesion microenvironment. The results also illustrate the advantage of using 3-D histology to reveal the previously unknown details of the neurovascular and endocrine links to the disease.