Normally, electrostatic-dependent mitochondria localization can cause a decrease/loss of mitochondrial membrane potential (MMP), leading to the corresponding abnormal behaviors. So, achieving subcellular organelle localization and imaging with as little interference on their physiological activity is of significance for understanding cell activity. Herein, we discover and demonstrate that "polarity" can independently act as a novel kind of target for labeling at the organelle level. On this basis, mitochondria and lysosomes are precisely fluorescently imaged by two kinds of polarity-targeted carbon dots (C-dots), respectively. The two C-dots, named C-dots-1 and C-dots-2, have almost identical size and morphology as well as surface chemistry. The subtle difference is their polarity property: both of them are amphiphilic, with 1.54 and 0.95 for the log P values. Different from commonly used cationic-based organelle probes, both of the two C-dots possess slightly negatively charged surfaces (ζ-potential values ∼ −2.5 to −7.5 mV) at physiological conditions. Interestingly, the C-dots-1 and C-dots-2 have the capacity for highly selectively labeling and imaging mitochondria and lysosomes, whether cancer cells or normal cells. Because the targeting processes do not rely on electrostatic attraction effects, the MMP is not changed during localization processes. So, the corresponding cell abnormal behaviors caused by MMP diminishing, for example, the autophagy phenomenon, can be effectively avoided.