Electrical coupling is vital to neural communication, facilitating synchronized activity among neurons. Despite its significance, the precise mechanisms governing the establishment of gap junction connections between specific neurons remain elusive. Here, we identified that the PVC interneuron in Caenorhabditis elegans forms gap junction connections with the PVR interneuron. The transcriptional regulator CFI-1 (ARID3) is specifically expressed in the PVC but not PVR interneuron. Reducing cfi-1 expression in the PVC interneuron leads to enhanced gap junction formation in the PVR neuron, while ectopic expression of cfi-1 in the PVR neuron restores the proper level of gap junction connections in the PVC neuron, along with the normal touch response. These findings unveil the pivotal role of CFI-1 in bidirectionally regulating the formation of gap junctions within a specific neuronal pair, shedding light on the intricate molecular mechanisms governing neuronal connectivity in vivo.