In this work, we investigated the mechanism for the stability of internally doped Cu:ZnSe aqueous nanocrystals (NCs). Some new findings are reported. First, the stability of NCs is governed by the probability of photoinduced holes being present on the NC surface, which can be adjusted by many experimental factors. The methods decreasing the probability of holes being present on the NC surface, for instance, making Cu impurities far away from the NC surface, storing NCs without oxygen, and enveloping of Cu:ZnSe NCs with a wide gap shell, can dramatically improve the stability of internally doped Cu:ZnSe NCs. Second, three distinguished stages, which appear during storage of NCs in oxygen under photoirradiation, are controlled by species of free Zn–MPA complexes in solution. Third, the peculiar alteration of the solution pH is observed during NC photooxidation, which is determined by two reactions. One produces OH–, and another consumes OH–.