Abstract Advanced atomic tracking techniques play a critical role in characterizing structural evolution, elucidating fundamental mechanisms of exotic phenomena and tailoring delicate properties. Thermally driven structural modulation in 2D crystals, such as the charge density wave (CDW), often leads to intriguing quantum properties, making them a valuable platform for exploring fundamental physics and potential device applications. However, despite their significance, experimental studies addressing atomic tracking of thermally‐driven structural evolution in 2D crystals have been limited. Herein, we utilize high‐accuracy variable‐temperature atomic tracking measurements with scanning tunneling microscopy (STM) to directly observe a series of structural transitions in a model 2D crystal, namely NbSe2. With the atomic tracking technique, we confirm the existence of the universal thermally‐driven CDW transition hysteresis between the heating and cooling cycles. This transition hysteresis, characterized by a constant temperature offset, represents a new phenomenon of structural evolution. Our findings provide a feasible method to track CDW transitions at the atomic scale in 2D crystals, significantly contributing to a better understanding and the potential modulation of these materials' functions in nanodevices.