Functional near-infrared spectroscopy (fNIRS) is an emerging non-invasive functional brain imaging technique, through detecting the changes of hemoglobin concentrations to investigate brain activities in various tasks. The aim of this study is to investigate the complexity of near-infrared spectroscopy signals during resting state and upper limb movements. Experimental study was designed by applying NIRS to collect the data especially for both healthy subjects and traumatic brain injury (TBI) patients. The modified multiscale entropy (MMSE) algorithm was employed to assess the complexity of fNIRS signals which may reflect the changes of brain activity when people underwent brain injury. The results that the mean MMSE of oxyhemoglobin values was lower in TBI patients compared to healthy subjects, indicated that MMSE was feasible to measure complexity of cerebral near-infrared spectroscopy signals in TBI patients, and that brain injury was associated with the decreased complexity of cerebrovascular reactivity. Moreover, measurement of complexity of brain signals has potential to provide significant guidance for rehabilitation.