We present particle counting ultrahigh-resolution optical Doppler tomography (pc-μODT) that enables accurate imaging of red blood cell velocities (νRBC) of cerebrovascular networks by detecting the Doppler phase transients induced by the passage of a RBC through a capillary. We apply pc-μODT to image the response of capillary νRBC to mild hypercapnia in mouse cortex. The results show that νRBC in normocapnia (νN = 0.72 ± 0.15 mm/s) increased 36.1% ± 5.3% (νH = 0.98 ± 0.29 mm/s) in response to hypercapnia. Due to uncorrected angle effect and low hematocrit (e.g., ∼10%), νRBC directly measured by μODT were markedly underestimated (νN ≈ 0.27 ± 0.03 mm/s, νH ≈ 0.37± 0.05 mm/s). Nevertheless, the measured νRBC increase (35.3%) matched that (36.1% ± 5.3%) by pc-μODT.