Enzyme inhibition based drug screening strategy has been widely employed for new drug discovery. But this strategy faces some challenges in practical application especially for the trace active compound screening from natural products such as the stability of enzyme and the sensitivity of screening approach. Inspired by the above, we for the first time demonstrate the self-assembly of α-glucosidase (GAA) and glucose oxidase (GOx) into one multi-enzymes-inorganic nanoreactor with hierarchical structure (flower shape). The hybrid enzyme nanoreactor enjoys the merits including the character of assembly line, the enhanced enzymatic activity and robust stability. The flower shape of enzyme nanoreactor possessed a bigger specific surface area, facilitating the trace GAA inhibitor detection. Based on the above, we proposed an enzyme nanoreactor mediated plasmonic sensing strategy for anti-diabetic drug screening. First, maltose was chosen as the substrate for GAA and the generated glucose were immediately utilized by GOx to generate H2O2, and finally, H2O2 etched the Ag nanoprism to round nanodiscs, resulting in the blue shift of surface plasmon resonance (SPR) absorption band. With the aid of hybrid enzyme nanoreactor guided SPR, the ultrasensitive screening of GAA inhibitor (i.e. anti-diabetic drug) can be realized with the detection limit of 5nM for acarbose. The proposed approach was successfully utilized for GAA inhibitor screening from natural products. We anticipate that the proposed sensing method may provide new insights and inspirations in the enzyme inhibition based drug discovery and clinical diagnosis.