Using a data sample corresponding to an integrated luminosity of 2.93fb$^{−1}$ taken at a center-of-mass energy of 3.773\,GeV with the BESIII detector operated at the BEPCII collider, we perform an analysis of the semi-leptonic decays $D^{0(+)}\to \pi^{-(0)}\mu^+\nu_\mu$. The branching fractions of $D^0\to \pi^-\mu^+\nu_\mu$ and $D^+\to \pi^0\mu^+\nu_\mu$ are measured to be $(0.272 \pm 0.008_{\rm stat.} \pm 0.006_{\rm syst.})\%$ and $(0.350 \pm 0.011_{\rm stat.} \pm 0.010_{\rm syst.})\%$, respectively, where the former is of much improved precision compared to previous results and the latter is determined for the first time. Using these results along with previous BESIII measurements of $D^{0(+)}\to \pi^{-(0)}e^+\nu_e$, we calculate the branching fraction ratios to be ${\mathcal R}^0\equiv {\mathcal B}_{D^{0}\to \pi^{-}\mu^+\nu_\mu}/{\mathcal B}_{D^{0}\to \pi^{-}e^+\nu_e}=0.922\pm 0.030_{\rm stat.}\pm0.022_{\rm syst.}$ and ${\mathcal R}^+\equiv {\mathcal B}_{D^{+}\to \pi^{0}\mu^+\nu_\mu}/{\mathcal B}_{D^{+}\to \pi^{0}e^+\nu_e}=0.964\pm 0.037_{\rm stat.}\pm0.026_{\rm syst.}$, which are compatible with the theoretical expectation of lepton flavor universality within 1.7σ and 0.5σ, respectively. We also examine the branching fraction ratios in different four-momentum transfer square regions, and find no significant deviations from the standard model predictions.