The correlations between the microstructure and nanomechanical properties of a series of thermal annealed Co thin films were investigated. The Co thin films were deposited on glass substrates using a magnetron sputtering system at ambient conditions followed by subsequent annealing conducted at various temperatures ranging from 300 °C to 800 °C. The XRD results indicated that for annealing temperature in the ranged from 300 °C to 500 °C, the Co thin films were of single hexagonal close-packed (hcp) phase. Nevertheless, the coexistence of hcp-Co (002) and face-centered cubic (fcc-Co (111) phases was evidently observed for films annealed at 600 °C. Further increasing the annealing temperature to 700 °C and 800 °C, the films evidently turned into fcc-Co (111). Moreover, significant variations in the hardness and Young's modulus are observed by continuous stiffness nanoindentation measurement for films annealed at different temperatures. The correlations between structures and properties are discussed.