Azimuthal anisotropies of muons from charm and bottom hadron decays are measured in Pb+Pb collisions at $\sqrt{s_\mathrm{NN}}= 5.02$ TeV. The data were collected with the ATLAS detector at the Large Hadron Collider in 2015 and 2018 with integrated luminosities of $0.5~\mathrm{nb}^{-1}$ and $1.4~\mathrm{nb^{-1}}$, respectively. The kinematic selection for heavy-flavor muons requires transverse momentum $4 < p_\mathrm{T} < 30$ GeV and pseudorapidity $|η|<2.0$. The dominant sources of muons in this $p_\mathrm{T}$ range are semi-leptonic decays of charm and bottom hadrons. These heavy-flavor muons are separated from light-hadron decay muons and punch-through hadrons using the momentum imbalance between the measurements in the tracking detector and in the muon spectrometers. Azimuthal anisotropies, quantified by flow coefficients, are measured via the event-plane method for inclusive heavy-flavor muons as a function of the muon $p_\mathrm{T}$ and in intervals of Pb+Pb collision centrality. Heavy-flavor muons are separated into contributions from charm and bottom hadron decays using the muon transverse impact parameter with respect to the event primary vertex. Non-zero elliptic ($v_{2}$) and triangular ($v_{3}$) flow coefficients are extracted for charm and bottom muons, with the charm muon coefficients larger than those for bottom muons for all Pb+Pb collision centralities. The results indicate substantial modification to the charm and bottom quark angular distributions through interactions in the quark-gluon plasma produced in these Pb+Pb collisions, with smaller modifications for the bottom quarks as expected theoretically due to their larger mass.