We study the gauged $U(1)_{L_mu-L_tau}$ scotogenic model with emphasis on latest measurement of LHCb $R_{K^{(*)}}$ anomaly and AMS-02 positron excess. In this model, neutrino masses are induced at one-loop level with $Z_2$-odd particles, i.e., right-handed neutrinos $N_ell(ell=e,mu,tau)$ and inert scalar doublet $eta$ inside the loop. Meanwhile, the gauged $U(1)_{L_mu-L_tau}$ symmetry is broken spontaneously by the scalar singlet $S$, resulting to the massive gauge boson $Z$. Provided certain couplings to quarks induced by heavy vector-like quarks, the gauge boson $Z$ would contribute to the transition $bto s mu^+mu^-$, hence explain the $R_{K^{(*)}}$ anomaly. As for the Majorana fermion DM $N$, the gauge boson $Z$ and the singlet Higgs $H_0$ will generate various annihilation channels, among which the $NNto ZZ$ and $NNto ZH_0(to ZZ)$ channel could be used to interpret the AMS-02 positron excess. We give a comprehensive analysis on model parameter space with consider various current constraints. The combined analysis shows that the $R_{K^{(*)}}$ anomaly and AMS-02 positron excess can be explained simultaneously.