This paper describes a micro-scale mapping of protein expression on endothelial tissue in an extracellular matrix (ECM)-based branched microchannel under mechanical stimuli. Our system mimics the heterogeneity in the distribution of complex mechanical stimuli applied to tissues in vivo by applying mechanical stimuli to a branched vascular model. We confirmed the up-regulation of gene expression levels in vascular endothelial cells(ECs) by stretch stress. We cultured ECs under complex mechanical stimuli, and visualized the distribution of mechanotransducer protein expression in the branched vascular model. We believe that our system could open a new door for the analysis of local cellular responses to mechanical stimuli.