Previous findings have demonstrated, in a rat model, that chronic cerebral hypoperfusion (CCH) decreases cortical cerebral blood flow (CBF) while Dl-3-n-Butylphthalide (DNB) accelerates the timely recovery of CBF. However, potential biomarkers, therapeutic targets, and underlying mechanisms for these processes are unclear. In this study, a solid-phase antibody microarray for simultaneously detecting multiple proteins was used to search cortex biotargets in CCH compared to a sham control group, and these results were further examined by biological functional analysis. After DNB treatment, western blot and immunostaining were used to verify candidate protein expression. Importantly, we identified seven proteins that may serve as novel biotargets contributing to CCH. The levels of Tie-2, CNTFRα, IL-4, IL-10, ITGAM, MDC, and TROY were uniquely altered in the CCH. The Tie-2 level was significantly decreased and identified in CCH 2 week (W), CCH 4 W and CCH 8 W. In addition, Ang-1 level and Ang-1/Ang-2 ratio were significantly decreased in CCH 2 W and CCH 4 W while Ang-2 level was increased in the CCH, whereas DNB treatment created the inverse effect to some extent. Moreover, the expression of VEGF and CD34 in the earlier stage of CCH and the diameters of bilateral vertebral arteries (VAs), were significantly enlarged by DNB treatment. Together, we found that the Ang-1/Ang-2/Tie-2 signaling axis was altered in the CCH rat cortex, and DNB treatment could timely regulate this angiopoietin/Tie signaling axis to promote neovascularization in early stages.