Due to their exceptional optical and magnetic properties, negatively charged nitrogen-vacancy (NV) centers in nanodiamonds (NDs) have been identified as an indispensable tool for imaging, sensing and quantum bit manipulation. The investigation of the emission behaviors of single NV centers at the nanoscale is of paramount importance and underpins their use in applications ranging from quantum computation to super-resolution imaging. Here, we report on a spin-manipulated nanoscopy method for nanoscale resolutions of the collectively blinking NV centers confined within the diffraction-limited region. Using wide-field localization microscopy combined with nanoscale spin manipulation and the assistance of a microwave source tuned to the optically detected magnetic resonance (ODMR) frequency, we discovered that two collectively blinking NV centers can be resolved. Furthermore, when the collective emitters possess the same ground state spin transition frequency, the proposed method allows the resolving of each single NV center via an external magnetic field used to split the resonant dips. In spin manipulation, the three-level blinking dynamics provide the means to resolve two NV centers separated by distances of 23 nm. The method presented here offers a new platform for studying and imaging spin-related quantum interactions at the nanoscale with super-resolution techniques.