The distinct in-plane lattice vibration dynamics and anisotropic electron–phonon interactions are important to detect the crystallographic orientation and polarization related properties in van der Waals layered crystals. This work presented a systematical exploration on the phonon modes of Ta2NiSe7 thin flakes with different thicknesses under variable temperatures, excitation wavelengths, and polarizations. All the Raman modes shifted linearly to the low wavenumber direction with increasing temperature. The maximum first-order temperature coefficient (χ) was −3.324 × 10–2 cm–1/K. The angle-resolved polarized Raman spectroscopy (ARPRS) of Ta2NiSe7 thin flakes showed a strong dependence of Raman intensity on the excitation laser wavelength and phonon symmetry/frequency, demonstrating the robust electron–phonon interaction and excitation energies dependent in-plane anisotropy in Ta2NiSe7 thin flakes. In addition, the crystallographic orientations of Ta2NiSe7 thin flakes were identified unambiguously by combination of the preferred cleavage edge with the one-step polarized Raman spectrum, despite their intricate carriers interaction and sensitive Raman mode intensity variation. These results revealed the complicated in-plane anisotropy in Ta2NiSe7 thin flakes and were helpful to determine the crystal orientation rapidly, which would promote the potential multifunctional device applications of these novel van der Waals layered crystals with similar low lattice symmetry.