Purpose <p>This study aimed to compare the distribution characteristics and clinical values of the intramuscular, epimuscular and subcutaneous fat depositions in lumbar areas in lumbar spinal stenosis (LSS) patients and healthy controls.</p> Methods <p>The study retrospectively reviewed 236 LSS patients undergoing posterior lumbar interbody fusion with follow-up visits. We also recruited 115 healthy controls from the community. All participants had undergone magnetic resonance imaging for the measurements of fat infiltration (FI) of the intramuscular fat and epimuscular fat of paraspinal extensor muscles (PEM, including multifidus [MF] and erector spinae [ES]), and subcutaneous fat tissue thickness. The evaluation of lumbar degeneration changes included intervertebral disk degeneration (IVDD) and Modic changes in healthy controls. Postoperative mechanical complications were measured at 1-year follow-up in LSS patients.</p> Results <p>The LSS patients presented with significantly higher intramuscular FI and epimuscular FI when compared with the healthy controls (<i>p</i> &lt; 0.001). The severe IVDD group exhibited significantly higher epimuscular FI than the mild-to-moderate IVDD group (<i>p</i> &lt; 0.01), and the Modic group exhibited significantly higher intramuscular FI (<i>p</i> &lt; 0.05). In terms of clinical outcomes, the patients with mechanical complications presented with higher intramuscular FI (<i>p</i> &lt; 0.05). In binary logistic regressions, the epimuscular FI was an independent factor of IVDD (OR = 1.209 [1.048–1.395], <i>p</i> = 0.009) for LSS patients, and the intramuscular FI was an independent factor of mechanical complications (OR = 1.053 [1.017–1.090], <i>p</i> &lt; 0.001).</p> Conclusion <p>The fat depositions in different lumbar areas might have specific distribution characteristics and different correlations to lumbar degenerative changes and clinical outcomes. Orthopedists should measure fat depositions in different lumbar areas separately during preoperative evaluation.</p>