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Charge density wave (CDW) is a spontaneous modulation of electron density, which is usually associated with periodic lattice distortion with the same wavelength. Such phenomenon is often observed in layered transition metal dichalcogenides (TMD), although its origin is still under debate. 1T-TMD TaTe₂ shows a CDW like phase transition around 170 K where new modulation of 3×3 superstructure forms. Magnetic susceptibility and resistivity show abnormal behavior at the phase transition, which is inconsistent with conventional model or example. Here, we use combination of scanning tunneling microscopy/spectroscopy, low energy electron diffraction, and density functional theory calculations to study the temperature dependence of CDW in undoped and Se doped TaTe₂ single crystals. We have observed a hidden phase with a distinct modulation, which can be stabilized by Se doping, and is less metallic than the 3×3 low temperature phase. Our results suggest a possible explanation to the mystery in transport properties, which provides new insight on the electron-lattice coupling associated with CDW phase transitions.