Mental fatigue is a key cause of chronic diseases and traffic accidents, which is difficult to be quantitatively evaluated. In order to non-intrusively detect fatigue state, an optical fiber sensing system is proposed, which is non-invasive and does not require direct contact with skin. The fiber sensor was fabricated through phase mask exposure method and packaged by sensitivity-enhanced structure, which can suppress transverse force and increase signal amplitude by 5%. A fatigue-inducing experiment was carried out, and the heartbeat signals of 20 subjects under different fatigue states were collected by the proposed sensing system. A series of heart rate variability indicators were calculated from the sensing signals, and their statistical significance for fatigue was analyzed. The experiment results showed that the values of SDNN and LF/HF increased significantly with subjects\' fatigue level. This study shows that the proposed fiber optic sensing system has practical value in fatigue state monitoring.