The study of first-order structural transformations has been of great interest to scientists in many disciplines. Expectations from phase-transition theory are that the system fluctuates between two equilibrium structures near the transition point and that the region of transition broadens in small crystals. We report the direct observation of structural fluctuations within a single nanocrystal using transmission electron microscopy. We observed trajectories of structural transformations in individual nanocrystals with atomic resolution, which reveal details of the fluctuation dynamics, including nucleation, phase propagation, and pinning of structural domains by defects. Such observations provide crucial insight for the understanding of microscopic pathways of phase transitions.