Aberrant expression of histone deacetylases (HDACs) is related to various types of cancer and is associated with increased proliferation of tumor cells. Hence, the detection of HDAC activities is of great significance for medical sciences as well as biological diagnostics. Herein, we report a hyperbranched polyester-based one-step fluorescent assay for HDAC. This assay system consists of two water-soluble components: the hyperbranched polyester coupled with the acetylated lysine groups (H40-Lys(Ac)) and the negatively charged TPE derivative bearing two sulfonic acid groups (TPE-2SO(3)(-)). HDAC triggers the deacetylation of H40-Lys(Ac), thereby turning the electroneutral polymer into the positively charged one. Consequently, complexation occurs between the positively charged polymer and the negatively charged TPE-2SO(3)(-), thereby leading to the formation of nanoaggregates due to electrostatic interaction. Eventually, the fluorescence enhancement as a result of AIE effect is achieved. This assay system is operable in aqueous media with very low detection limit of 25 ng/mL. The system is capable of detecting HDAC in such biological fluid as serum, and this strategy may provide a new and effective approach for enzyme assay.