The development of data analysis methods will be a critical factor for promoting the application of NIRS technology. 7, 8 Current NIRS studies usually analyze only local changes in brain regions, with limited characterization of the brain’s functional architecture. 5, 6 However, the current application of NIRS in functional brain imaging is just the tip of the iceberg the potential is far from fully exploited. 1, 2 Because NIRS places fewer limitations on the subjects and environment than other functional neuroimaging methods such as functional magnetic resonance imaging (fMRI) and positron emission tomography (PET), 3, 4 it has been widely applied in the cognitive and clinical research field. Near-infrared spectroscopy (NIRS) is a developing and promising technology that monitors brain activity noninvasively and cheaply by measuring cerebral hemodynamic responses. This study demonstrates that the NIRS-based connectivity can reveal the functional architecture of the brain more comprehensively than traditional activation, helping to better utilize the advantages of NIRS. The results showed increased information flow from the left to the right hemispheres for the incongruent versus the neutral task, indicating a leading role of the left PFC. Granger causality was used to evaluate the effective connectivity between hemispheres. However, functional connectivity was more sensitive than activation for identifying hemispheric lateralization. In agreement with activation analysis, functional connectivity analysis revealed leftward lateralization for the Stroop effect and correlation with behavioral performance. Spearman correlation analysis was used to examine the relationship between behavioral performance and activation/functional connectivity, respectively. Wavelet transform coherence was used to assess intrahemispheric functional connectivity. Hemispheric lateralization was examined by employing traditional activation and novel NIRS-based connectivity analyses simultaneously. In this study, we measured hemodynamic activity of the prefrontal cortex (PFC) during a color-word matching Stroop task using NIRS. Developing data analysis methods to effectively extract meaningful information from collected data is the major bottleneck in popularizing this technology. Near-infrared spectroscopy (NIRS) is a developing and promising functional brain imaging technology.