Functional near-infrared spectroscopy (fNIRS) was used to explore the effects of sedentary behavior on the brain functional connectivity characteristics of college students in the resting state after recovering from Corona Virus Disease 2019 (COVID-19). Twenty-two college students with sedentary behavior and 22 college students with sedentary behavior and maintenance of exercise habits were included in the analysis; moreover, 8 ​min fNIRS resting-state data were collected. Based on the concentrations of oxyhemoglobin (HbO) and deoxyhemoglobin (HbR) in the time series, the resting-state functional connection strength of the two groups of subjects, including the prefrontal cortex (PFC) and the lower limb supplementary motor area (LS), as well as the functional activity and functional connections of the primary motor cortex (M1) were calculated. The following findings were demonstrated. (1) Functional connection analysis based on HbO demonstrated that in the comparison of the mean functional connection strength of homologous regions of interest (ROIs) between the sedentary group and the exercise group, there was no significant difference in the mean functional strength of the ROIs between the two groups ( ). In the comparison of the mean functional connection strengths of the two groups of heterologous ROIs, the functional connection strengths of the right PFC and the right LS ( ), the left LS ( ), and the right M1 ( ) in the sedentary group were significantly greater. The functional connection strength between the left PFC and the right LS ( ) and the left LS ( ) was significantly greater. Additionally, the functional connection strength between the right LS and the right M1 ( ) and the left LS ( ) was significantly greater. (2) Functional connection analysis based on HbR demonstrated that there was no significant difference in functional connection strength between the sedentary group and the exercise group ( ) or between the sedentary group and the exercise group ( ). Similarly, there was no significant difference in the mean functional connection strength of the homologous and heterologous ROIs of the two groups. Additionally, there was no significant difference in the mean ROIs functional strength between the two groups ( ). Experimental results and graphical analysis based on functional connectivity indicate that in this experiment, college student participants who exhibited sedentary behaviors showed an increase in fNIRS signals. Increase in fNIRS signals among college students exhibiting sedentary behaviors may be linked to their status post-SARS-CoV-2 infection and the sedentary context, potentially contributing to the strengthened functional connectivity in the resting-state cortical brain network. Conversely, the fNIRS signals decreased for the participants with exercise behaviors, who maintained reasonable exercise routines under the same conditions as their sedentary counterparts. The results may suggest that exercise behaviors have the potential to mitigate and reduce the impacts of sedentary behavior on the resting-state cortical brain network.