Microscopic swimmers, both living and synthetic, often dwell in anisotropic viscoelastic environments. The most representative realization of such an environment is water-soluble liquid crystals. Here, we study how the local orientation order of liquid crystal affects the motion of a prototypical elliptical microswimmer. In the framework of well-validated Beris-Edwards model, we show that the microswimmer’s shape and its surface anchoring strength affect the swimming direction and can lead to reorientation transition. Furthermore, there exists a critical surface anchoring strength for non-spherical bacteria-like microswimmers, such that swimming occurs perpendicular in a sub-critical case and parallel in super-critical case. Finally, we demonstrate that for large propulsion speeds active microswimmers generate topological defects in the bulk of the liquid crystal. We show that the location of these defects elucidates how a microswimmer chooses its swimming direction. Our results can guide experimental works on control of bacteria transport in complex anisotropic environments.