In two-dimensional materials, structure difference induces the difference in phonon dispersions, leading to the anisotropy of in-plane thermal transport. Here, we report an exceptional case in layered PdSe2, where the bonding, force constants, and lattice constants are nearly-equal along the in-plane crystallographic axis directions. The phonon dispersions show significant differences between the Gamma-X and Gamma-Y directions, leading to the anisotropy of in-plane thermal conductivity with a ratio up to 1.8. Such anisotropy is not only unexpected in equilaterally structured (in-plane) materials but also comparable to the record in the non-equilaterally structured material reported to date. By combining inelastic X-ray scattering and first-principles calculations, we attribute such anisotropy to the low-energy phonons along Gamma-X, in particular, their lower group velocities and avoided-crossing behavior. The different bucking structures between a- (zigzag-type) and b-axis (flat-type) are mainly responsible for the unique phonon dynamics properties of PdSe2. The present results illustrate the unusual thermal conduction mechanism of the equilaterally structured materials and provide valuable insights on thermal management in electronic devices.