Surface electromyography (sEMG) studies have indicated that chronic low back pain (cLBP) involves altered electromyographic activity and morphological structure of the lumbar multifidus (LM) beyond pain perception; however, most studies have evaluated the superficial lumbar multifidus. It is difficult to record electromyography (EMG) signals from the deep multifidus (DM) to determine the neuromuscular activation patterns, making it difficult to determine the relationship between functional and structural changes in cLBP. We developed a novel method to record intramuscular EMG signals in the DM based on the sEMG system and fine-wire electrodes. We measured EMG signals of the DM in 24 cLBP patients and 26 pain-free healthy controls to identify changes in neuromuscular activation. We also used ultrasound to measure DM muscle thickness, cross-sectional area, and contraction activity to identify potential relationships between EMG activity and structural damage. cLBP patients had decreased average EMG and root mean square, but increased median frequency and mean power frequency. Average EMG was positively correlated with contractile activity, but not statistically correlated with noncontractile anatomical abnormalities. Our results suggest that cLBP alters the neuromuscular activation patterns and morphological structure of the contractile activity of the DM, providing insights into the mechanisms underlying pain perception.