The nitrogen−vacancy (NV) center in diamond gains its versatility when negatively charged (NV−) but is mediocre when neutrally charged. Particularly, the charge states of NV centers are convertible under optical pumping and during the dark intervals, whose dynamics are mixed with the NV−s’ spin polarizations and relaxations, making them difficult to detect. Here, a microwave‐pulses‐assisted charge state dynamics (CSD) measurement method of NV centers in the dark time (DT) is proposed. The microwave pulses are designed to manipulate the populations of the NV−s’ ground state spin triplets (qutrit) to the equilibrium state before the DT. Thus, the longitudinal relaxations of the qutrit are balanced, and pure CSD can be detected. Interestingly, in an annealed bulk diamond, not only the traditional tunneling‐induced fast exponential CSD are observed, but also a slow and long‐term recharging process, which is probably attributed to the exchanging of the electrons between NV centers and the high‐energy‐level charge traps such as vacancy clusters. Furthermore, results demonstrate a 40% increase in NV−s’ contrast by properly extending the recharging DT. These results are significant for the in‐depth study of the NV centers’ CSD and can improve the sensing abilities of the NV− ensemble.