Chronic low back pain (LBP) is a common musculoskeletal disorder and is often accompanied by functional leg length inequality (FLLI). However, little was known about the effects of gluteal muscle control training in patients with LBP and FLLI. This study was designed to investigate the effects of gluteal control training in patients with LBP and FLLI. This is a double-blinded, randomized controlled study design. Forty-eight LBP patients with FLLI were randomized to the gluteal control training (GT) (47.58 ± 9.42 years) or the regular training (RT) (47.38 ± 11.31 years) group and received allocated training for six weeks. The outcome measures were pelvic inclination (PI), ilium anterior tilt difference (IATD), FLLI, visual analogue scale (VAS), patient specific-functional scale (PSFS), Oswestry disability index (ODI), hip control ability, global rating of change scale (GRoC), and lower extremity strength and flexibility. The intervention effects were compared using two-way repeated measures analysis of variance and chi-square tests with α = 0.05. The results indicated that the GT group showed greater improvement (P < 0.01) in PI (1.03 ± 0.38∘ vs. 1.57 ± 0.51∘), IATD (0.68 ± 0.66∘ vs. 2.31 ± 0.66∘), FLLI (0.3 ± 0.22 vs. 0.59 ± 0.13 cm), VAS (1.41 ± 1.32 vs. 3.38 ± 1.51), hip control ability (2.20 ± 0.45 vs. 0.89 ± 0.74), GRoC at 3rd and 6th week as compared to the RT group. Hip strength and flexibility also improved more in the GT group (P < 0.05). In conclusion, gluteal control training was more effective in improving low back pain and dysfunctions, and should be integrated in the management plan in patients with LBP and FLLI.