We report a quantum dot (QD) photo-modulation route initiated by photo-absorption by QDs which needs relatively weak light at long wavelengths. The photo-excited electrons in QD are designed to transfer to crystal violets (CVs) on QD surface. CVs on QD acted as an efficient fluorescence quencher, however upon continuous excitation the electron-doped CVs degraded into a non-quencher which in turn activated the QD. Multi-color on-demand photo-patterning was demonstrated using two-color QD-CVs in solid films. The QD-CV probes were introduced into cells, and the visible light excitation yielded photo-modulation nearly ten folds in intracellular environment. Exploiting the stochastic PL burst of QD-CVs and multiplexing capability of QDs, simultaneous multi-color super-resolution localizations were demonstrated. On the other hand, recent technological advances have expanded fluorescence (FL) imaging into the second near-infrared region (NIR-II; wavelength = 1000–1700 nm), providing high spatial resolution through deep tissues. However, bright and compact fluorophores are rare in this region, and sophisticated control over NIR-II probes has not been fully achieved yet. We report an enzyme-activatable NIR-II probe that exhibits FL upon matrix metalloprotease activity in tumor microenvironment. Bright and stable PbS/CdS/ZnS core/shell/shell QDs were synthesized as a model NIR-II fluorophore, and activatable modulators were attached to exploit photo-excited electron transfer (PET) quenching. Using a colon cancer mouse model, the probe demonstrated selective FL activation at tumor sites, with three-fold signal enhancement in 10 min.