The design of tunable luminescent biomaterials with large Stokes shifts is usually pursued by a twisted intramolecular charge transfer (TICT) effect with switchable emission colors in response to various external stimuli. However, such a strategy is usually realized in conjugated molecules containing benzene or its derivatives and consequently suffers from poor biocompatibility. In this work, a hyperbranched polysiloxane (HBPSi)-based non-conjugated fluorescent polymer with TICT and aggregation-induced emission (AIE) features is developed, and its luminescent properties, fluorescence mechanism, and potential applications are investigated. Initially, the non-conjugated HBPSi exhibits remarkable AIE characteristics due to the formation of through-space conjugation. With the introduction of the sulfur atom, a non-conjugated D-A type AIE material, HBPSi-Cys, that exhibits a dual-state emission with a large Stokes shift of 213 nm, is obtained. The correlation of the lower-energy emission band with solvent polarity suggests the existence of the TICT state. TICT and AIE characteristics direct different properties of HBPSi-Cys, with TICT regulating solvatochromic emission wavelengths and AIE manipulating the emission intensity with a compensation effect. Density functional theory calculations reveal that the non-conjugated D-A structure in HBPSi-Cys was formed across the silicon bridge, with auxochromic sulfhydryl groups and adjacent amide groups as acceptor units and amine and hydroxyl groups as donor units. Additionally, the AIE-active HBPSi could be utilized as a fluorescent probe for the analysis of metal ions. After grafting the AS1411 aptamer to HBPSi-Cys as the recognition motif, HBPSi-Apt possesses excellent targeted bioimaging, drug loading, pH/GSH dual-responsive drug release, and visualized drug delivery performance. This work provides a new way to design functional AIE polymers with tunable optical properties, and the synthesized HBPSi-Cys shows great potential as a smart fluorescent biomaterial.