To solve the problem of potential food safety hazards and environmental hazards associated with artificial sweeteners as emerging pollutants, an eco-friendly aerogel (PSPI-GO) consisting of polyethyleneimine-modified soy protein isolate (PSPI) and graphene oxide (GO) was constructed to efficiently eliminate saccharin (SAC), a typical artificial sweetener in water. The equilibrium adsorption capacity of PSPI-GO for SAC was 293 mg/g, which removed 91% of SAC. PSPI-GO exhibited a highly porous structure and excellent renewability. Multiple quantum chemical theory calculations including electrostatic potential (ESP), frontier molecular orbital (FMO), independent gradient model based on Hirshfeld partition (IGMH), and Hirshfeld surface analysis (HSA) further elucidated that electrostatic attraction, hydrogen bonding, and inter-molecular interactions dominate the adsorption process. This work achieved high-value utilization of SPI while providing a new strategy for efficient removal of SAC. The research strategy integrating analysis of macroscopic mass transfer mechanisms and visualization of the adsorption mechanism provides a new perspective for in-depth understanding of inter-molecular adsorption behavior.