Developing a simple yet powerful method for enzyme activity monitoring is of great significance in the early diagnosis of diseases. Herein, we designed a precise spectral overlap-triggered inner filter effect (IFE) fluorescence sensing platform for alkaline phosphatase (ALP) detection. ALP could catalyze hydrolysis of p-nitrophenylphosphate (PNPP) to generate p-nitrophenol (PNP) and PNP acts as a powerful acceptor in IFE reaction system to influence the excitation of fluorescent donors. Based on this principle, a standardized procedure was proposed for rational screening of high-performance donor/acceptor pairs to maximize IFE efficiency. The results proved that perfect spectral overlap and high quantum yield of fluorescent donors synergistically contribute to maximizing IFE efficiency. In this case, a high quantum yield of 51.7% of the arginine surface-engineered gold nanoclusters (Arg/ATT-AuNCs) produced perfect spectral overlap with PNP and achieved maximal IFE efficiency, which was eventually selected as fluorescent signal tag for ALP detection. The Arg/ATT-AuNCs-based approach achieved ultrasensitive detection of ALP with a detection limit of 0.0062 U/L, which exhibited 4.2–25.8-fold improvement compared to other donors. Furthermore, the accuracy and reliability of established method in real human serum samples were verified by spiking analysis and commercial kits, thus providing a promising platform for monitoring ALP. This work aims to provide a standardized procedure for rational screening high-performance donor/acceptor pairs and to develop an ultrasensitive IFE sensing platform for biomarkers detection, which will open up a promising horizon for other biomarkers detection in clinical diagnostics.