In our previous work [ , Phys. Rev. D 88, 074021 (2013)], it has been found that sizable charmonium events can be produced via the channel at the suggested super factory, where represents the dominant color-singlet -wave and -wave charmonium states , , and (, 1, 2), respectively. As an important step forward, in the present paper, we present a next-to-leading order (NLO) QCD analysis within the framework of nonrelativistic QCD. Different from the case of factory in which the single charmonium production is dominated by the channel via a virtual photon, at the super factory, its cross section is dominated by the channel via a boson. Estimations up to NLO level are done under the condition of both the factory and the super factory. We observe that the NLO distributions have the same shapes as those of LO distributions, but their differences are sizable. This indicates that a NLO calculation is necessary and important to achieve a more accurate estimation. Due to the boson resonance effect, at the super factory with a high luminosity up to , when summing all the color-singlet states’ contributions together, one may observe about charmonium events via the channel in one operation year. Then, such a super factory could provide another useful platform to study the charmonium properties, even for the higher charmonium states.