In vivo quantitative measurement of biodistribution plays a critical role in the drug/probe development and diagnosis/treatment process monitoring. In this work, we report a probe, named AIE-SRS-Mito, for imaging mitochondria in live cells via fluorescence (FL) and stimulated Raman scattering (SRS) imaging. The probe features an aggregation-induced emission (AIE) characteristic and possesses an enhanced alkyne Raman peak at 2223 cm–1. The dual-mode imaging of AIE-SRS-Mito for selective mitochondrion-targeting was examined on a homemade FL–SRS microscope system. The detection limit of the probe in the SRS imaging was estimated to be 8.5 μM. Due to the linear concentration dependence of SRS and inertness of the alkyne Raman signal to environmental changes, the intracellular distribution of the probe was studied, showing a local concentration of >2.0 mM in the mitochondria matrix, which was >100-fold higher than the incubation concentration. To the best of our knowledge, this is the first time that the local concentration of AIE molecules inside cells has been measured noninvasively and directly. Also, the nonquenching effect of such AIE molecules in cell imaging has been verified by the positive correlation of FL and SRS signals. Our work will encourage the utilization of SRS microscopy for quantitative characterization of FL probes or other nonfluorescent compounds in living biological systems and the development of FL–SRS dual-mode probes for specific biotargets.