Within the framework of the non-relativistic QCD (NRQCD), we make a systematical study of the yields and polarizations of $J/psi$ and $Upsilon$ via $gamma gamma to J/psi(Upsilon)+gamma+X$ in photon-photon collisions at the Circular Electron Positron Collider (CEPC), up to $mathcal O(alpha^{3}alpha_s)$. We find that this process at CEPC is quite clean, namely the direct photoproduction absolutely dominate over the single- and double- resolved processes, at least 2 orders of magnitude larger. It is found that the next-to-leading order (NLO) QCD corrections will significantly reduce the results due to that the virtual corrections to $^3S_1^1$ is large and negative. For $J/psi$, as $p_t$ increases, the color octet (CO) processes will provide increasingly important contributions to the total NLO results. Moreover the inclusion of CO contributions will dramatically change the polarizations of $J/psi$ from toally transverse to longitudinal, which can be regarded as a distinct signal for the CO mechanism. However, for the case of $Upsilon$, the effects of the CO processes are negligible, both for yields and polarizations. For $J/psi$, the dependence of the yields on the value of the renormalization scale $mu_r$ is moderate, while significant for the polarization. The impact of the variation of $mu_{lambda}$ is found to be relatively slight. As for the case of $Upsilon$, the uncertainties of $mu_{r}$ and $mu_{lambda}$ just bring about negligible effects. The future measurements on this semi-inclusive photoproductions of $J/psi(Upsilon)+gamma+X$, especially on the polarization parameters of $J/psi$, will be a good laboratory for the study of heavy quarkonium production mechanism and helpful to clarify the problems of the $J/psi$ polarization puzzle.
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