The nanomechanical properties and nanoindentation responses of bismuth selenide (Bi2Se3) thin films are investigated in this study. The Bi2Se3 thin films are deposited on c-plane sapphire substrates using pulsed laser deposition. The microstructural properties of Bi2Se3 thin films are analyzed by means of X-ray diffraction (XRD). The XRD results indicated that Bi2Se3 thin films are exhibited the hexagonal crystal structure with a c-axis preferred growth orientation. Nanoindentation results showed the multiple “pop-ins” displayed in the loading segments of the load-displacement curves, suggesting that the deformation mechanisms in the hexagonal-structured Bi2Se3 films might have been governed by the nucleation and propagation of dislocations. Further, an energetic estimation of nanoindentation-induced dislocation associated with the observed pop-in effects was made using the classical dislocation theory.