The functional networks of the brain play a crucial role in cognitive impairment in temporal lobe epilepsy (TLE). However, it is unclear how abnormal functional homotopy alters effective connectivity. Therefore, we investigated the neuroimaging features of the right TLE (rTLE) and their correlation with cognitive impairment using voxel-mirrored homotopic connectivity (VMHC), Granger causality analysis (GCA), and neuropsychological tests. The data from twenty-seven rTLE patients and twenty-seven healthy controls were used to construct a functional network and analyze the relationship between connectivity and cognition. VMHC analysis revealed that the homotopy was disrupted in the middle frontal gyrus (MFG), middle temporal gyrus, dorsolateral superior frontal gyrus, and supramarginal gyrus (SMG) in rTLE group. In GCA, the abnormal connectivity with brain areas was observed in several functional subnetworks, such as the default mode network, sensorimotor network, and visual network. Besides, both phasic and tonic alertness reaction times were positively correlated with the connectivity from the left MFG to the left precentral gyrus (PreCG), from the left SMG to the right PreCG, and from the left SMG to the right supplementary motor area (SMA). Executive control effect reaction time was positively correlated with the connectivity from the left MFG to the left calcarine fissure surrounding cortex. Our findings indicated that the disordered effective connectivity can exacerbate the cognitive impairment and the compensatory effect of functional network can improve cognitive performance in rTLE.