The study was aimed to investigate the clinical effect and mechanism of Shugan-Jieyu-Jianpi (SGJYJP) formula for the treatment of irritable bowel syndrome (IBS) combined with non-alcoholic fatty liver disease (NAFLD). The clinical efficacy of SGJYJP was evaluated in 54 patients with IBS-NAFLD. The potential molecular mechanism of SGJYJP formula was investigated by network pharmacology. Animal models were constructed to explore the related mechanism. From clinical studies, the total effective rate of patients in SGJYJP group was significantly higher than that in pinaverium group. The protein expression of TGFB1 was declined in IBS-NAFLD rats, together with the increased expression of PTGS2 and TNF, which was abolished by SGJYJP treatment. SGJYJP significantly reduced the expression of TNF signalling related molecules of TRAF2, caspase-8, and elevated the expression of Bcl-xl in IBS-NAFLD animal models. SGJYJP may exert therapeutic effect on IBS-NAFLD by targeting PTGS2, TGFB1, and TNF genes and TNF signalling.