Abstract Background: In patients diagnosed with nonspecific chronic low back pain (NCLBP), discernable discrepancies in pain perception have been observed. This study endeavors to assess alterations in left thalamic metabolites in patients with NCLBP following spinal manipulation, utilizing proton magnetic resonance spectroscopy (1H-MRS). Materials and Methods: A total of 16 individuals diagnosed with NCLBP and 16 healthy individuals volunteers of normal constitution (aged between 20 and 50 years) were recruited. All participants exhibited right-hand dominance. Before commencement of therapeutic intervention and at a 5-week interval thereafter, functional and radiological assessments were undertaken (Oswestry Disability Index, numerical rating scale, and 1H-MRS). The values were compared using independent and paired t tests. Results: Following spinal manipulation, the patients experienced notable reductions in pain and disability (P < 0.05). The treatment group demonstrated significant increases in N-acetyl aspartate (NAA), choline (Cho), myo-inositol (Mio), and glutamate and glutamine (Glx) in the left thalamus region post-treatment compared with the baseline measures (P < 0.05). Before treatment, NAA, Cho, Glx, and Mio levels were significantly lower in the left thalamus of the patients compared with healthy subjects (P < 0.05). However, no significant differences in terms of metabolites were observed between the healthy control group and the patients after the treatment. Conclusion: In patients presenting with NCLBP, spinal manipulation has been observed to exert an effect on the brain, thereby inducing changes in thalamic metabolites.