Abstract Background The serum creatinine-to-cystatin C ratio (Scr/Scys) has been suggested as a surrogate marker of muscle mass and a predictor of adverse outcomes in many diseases. However, the prognostic value of Scr/Scys in patients with type 2 diabetes mellitus (T2DM) is unknown. The aim of this study is to assess the prognostic value of Scr/Scys in patients with T2DM. Methods In this retrospective observational study, we enrolled 3668 T2DM patients undergoing coronary angiography (CAG). Serum creatinine (Scr) and serum cystatin C (Scys) levels were measured at admission. The study population was separated into low muscle mass (low-MM) and normal muscle mass (normal-MM) groups by Scr/Scys cut-off point. The association between muscle mass and long-term all-cause mortality was examined using Cox regression analysis. Results During a median follow-up of 4.9 (3.0–7.1) years, a total of 352 (9.6%) patients died. The mortality was higher in patients with low-MM as compared with patients with normal-MM (11.1% vs. 7.3%; p