Objective To investigate the changes of brain activation and brain network connectivity in patients with spinal cord injury (SCI). Methods A total of 20 patients with SCI were selected from Qilu Hospital of Shandong University from January to October 2021, including 8 patients with simple lower extremity involvement (paraplegia group) and 12 patients with all limbs involvement (tetraplegia group), and 10 healthy controls with matched baseline data with the SCI group were included in the same period. Functional near⁃infrared spectroscopy (fNIRS) was used to collect the data of cerebral oxyhemoglobin (HbO2) in the bilateral prefrontal lobe (LPFC/RPFC), motor cortex (LMC/RMC) and occipital lobe (LOL/ROL). The resting HbO2 β values was calculated by generalized linear model to evaluate the activation degree of the cerebral cortex covered by different detection channels, the correlation between HbO2 β values was calculated by Pearson correlation analysis and partial correlation to analysis different detection channels [partial correlation coefficient (r) was defined as functional connectivity strength] to evaluate the functional connectivity of the brain network. Results 1) Degree of brain activation: compared with the control group, the HbO2 β values corresponding to channel 2 (t=⁃2.482, P=0.020), channel 8 (t=⁃3.315, P=0.003) and channel 16 (t=⁃2.738, P=0.011) was increased in the tetraplegia group, while the HbO2 β value corresponding to channel 25 was decreased (t=2.104, P=0.045), and the HbO2 β value of channel 8 was increased (t=⁃2.475, P=0.020) in paraplegia group. Compared with the tetraplegia group, the HbO2 β values in channel 17 (t=2.552, P=0.017) and channel 25 (t=2.342, P=0.027) were increased in the paraplegia group. The value of HbO2 β in the left prefrontal lobe of tetraplegia group was significantly higher than that of control group (t=2.652, P=0.013). 2) The number of functional connections between different channels and cerebral cortex: the proportion of channels related to motor cortex in different groups was 94.12% in the paraplegia group (32/34), 82.76% in the tetraplegia group (24/29), and only 74.36% in the control group (29/39). 3) Functional connectivity strength in the brain: compared with the control group, the functional connectivity strength in the right motor area was weakened in both the paraplegia group (t=4.572, P=0.000) and the tetraplegia group (t=4.822, P=0.000). Conclusions There are abnormalities in resting brain activation and functional connectivity of brain network after SCI, which are manifested as local enhancement of spontaneous neural activity in some brain regions and abnormal functional connectivity in cerebral cortices and brain regions