Great attention is paid to that stimulus response of materials, which is a prerequisite for energy harvesting applications. Driven by advances in nanotechnology, the atomic motions, involved in phase transitions and associated with stimulus responses, require detailed investigation on the nanoscale. Recently, strain engineering of BiFeO3 (BFO) has become the subject of broad research interest due to its promising potential in energy conversion applications, such as piezoelectric, pyroelectric and shape memory effect (SME) devices. In this study, an excellent pyroelectric response is associated with reversible phase transitions in mixed-phase BFO films using thermal stimuli. Using an in situ high-resolution transmission electron microscope (HRTEM), we observed that phase transition between rhombohedral-like (R-like) and tetragonal-like (T-like) BFO involved the migration of the phase boundary, which is a prerequisite for the growth of the T-like phase and requires an intermediate phase. Moreover, the origin of the phase transition is attributed to competition between thermodynamic stability and substrate-induced strain, as suggested by phase-field simulations. The results provide a fundamental understanding of the atomic processes that underlie the stimulus response of the strained BFO films and demonstrate the potential of this extraordinary material for novel energy harvesting applications.