The assessment of glutathione (GSH) levels is associated with early diagnostics and pathological analysis for various disorders. Among all kinds of techniques for detecting GSH, the colorimetric assay relying on the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) catalyzed by many nanomaterials with peroxidase-like activity attracts increasing attention owing to its outstanding merits, such as high sensitivity and high selectivity. However, the aggregation between the nanomaterials severely hinders the entrance of TMB into the “active site” of these peroxidase mimics. To address this problem, the D-amino acid incorporated nanoflowers possessing peroxidase-like activity with a diameter of 10–15 μm, TMB and H2O2 were employed to establish the detection system for determining the level of glutathione. The larger diameter size of the hybrid nanoflowers substantially averts the aggregation between them. The results confirm that the hybrid nanoflowers detection system presents a low limit of detection, wide linear range, perfect selectivity, good storage stability and desired operational stability for the detection of GSH relying on the intrinsic peroxidase-like activity and favorable mechanical stability of the hybrid nanoflowers, indicating that the hybrid nanoflowers detection system has tremendous application potential in clinical diagnosis and treatment.