Introduction. The transversus abdominis (TVA) and multifidus (MF) muscles are the main segmental spinal stabilizers that are controlled by the primary motor cortex of the brain. However, relocations of the muscle representation in the motor cortex may occur after chronic lower back pain (cLBP); it still needs more evidence to be proven. The current study was aimed at applying transcranial magnetic stimulation (TMS) to investigate the changes of representation of TVA and MF muscles at the cortical network in individuals with cLBP. Methods. Twenty-four patients with cLBP and 12 age-matched healthy individuals were recruited. Responses of TVA and MF to TMS during muscle contraction were monitored and mapped over the contralateral cortex using a standardized grid cap. Maps of the center of gravity (CoG), area, volume, and latency were analyzed, and the asymmetry index was also computed and compared. Results. The locations of MF CoG in cLBP individuals were posterior and lateral to the CoG locations in healthy individuals. In the healthy group, the locations of TVA and MF CoG were closed to each other in both the left and right hemispheres. In the cLBP group, these two locations were next to each other in the right hemisphere but discrete in the left hemisphere. In the cLBP group, the cortical motor map of TVA and MF were mutually symmetric in five out of eleven (45.5%) subjects and leftward asymmetric in four out of ten (40.0%) subjects. Conclusions. Neural representations of TVA and MF muscles were closely organized in both the right and left motor cortices in the healthy group but were discretely organized in the left motor cortex in the cLBP group. This provides strong support for the neural basis of pathokinesiology and clinical treatment of cLBP.