Removal of short-chain per- and polyfluoroalkyl substances (PFAS) represents a unique challenge in comparison to the long-chain homologs. In this study, a series of functionalized periodic mesoporous organosilica (PMO) materials with tunable molar ratio of fluoroalkyl to amine functional groups were developed and used as platform adsorbents to investigate the adsorption behavior of short-chain PFAS, with a focus on perfluorobutanoic acid (PFBA). Modification with fluoroalkyl group substantially enhanced the adsorption affinity of PFBA with the functionalized PMO materials. Adsorption free energy analysis suggested that although electrostatic interactions were more predominant in PFBA adsorption, modification of PMOs with increased fluoroalkyl group loadings increased the non-electrostatic interactions with PFBA, resulting in more favorable PFBA adsorption. The optimal functionalized PMO showed fast PFBA adsorption kinetics, excellent PFBA removal efficiency in various water chemistry conditions, and can be regenerated and reused for numerous cycles with methanol/water mixture containing 500-mM NH3·H2O as regenerant. Furthermore, the optimal functionalized PMO showed robust performance for the removal of PFAS mixtures under complex natural water matrix. Results of this study suggested the important role of non-electrostatic interactions in enhancing the removal of short-chain PFAS and can provide mechanistic insights into guiding the design of improved adsorbents for PFAS removal.