We report the observation of a large anisotropic topological Hall effect (THE) in the hexagonal non-collinear magnet Fe5Sn3 single crystals. It is found that the sign of the topological Hall resistivity is negative when a magnetic field H perpendicular to the bc-plane (Hperp bc-plane), however, it changes form negative to positive when H parallel to the c-axis (Hparallel c-axis). The value of topological Hall resistivity increased with the increasing temperature and reached approximately -2.12 muOmega cm (Hperp bc-plane) and 0.5 muOmega cm (Hparallel c-axis) at 350 K, respectively. Quantitative analyses of the measured data suggest that the observed anisotropic THE may originate from the opposite scalar spin chirality induced by the magnetic fields perpendicular and parallel to the c-axis, respectively.