Glaucoma eye drops often suffer from low bioavailability due to rapid drug release and poor ocular retention. This study aimed to address these challenges by developing betaxolol hydrochloride-loaded mesoporous silica polyacrylic resin microspheres (BH@MCM-41 MPs) and comparing their safety, ocular retention, and intraocular pressure (IOP)-lowering efficacy with previously reported betaxolol hydrochloride-loaded montmorillonite polyacrylic resin microspheres (BH@MMT MPs), BH solution, and commercially available Betoptic®. Both BH@MCM-41 MPs and BH@MMT MPs demonstrated sustained drug release over 12 h and good biocompatibility. The impact of physicochemical particle characteristics on micro-interactions with tear film mucins and corneal epithelial cells was investigated. BH@MCM-41 MPs exhibited significantly higher mucin-binding capacity compared to BH@MMT MPs, with approximately double the binding at mucin concentrations over 0.4 mg·mL-1. Rose Bengal assays indicated a more hydrophobic surface for BH@MCM-41 MPs, with a binding constant (K) of 88.51, compared to 69.84 for BH@MMT MPs. In addition, these positively charged microspheres demonstrated prolonged precorneal retention, with BH@MCM-41 MPs achieving 58.17 minutes, compared to 44.49 minutes for BH@MMT MPs. Tear pharmacokinetics further confirmed the extended precorneal residence time of these formulations. Ex vivo corneal permeation studies revealed that the hydrophobic surface of BH@MCM-41 MPs enhanced interaction with corneal epithelial cells, promoting drug release and permeation. The area under the IOP reduction curve (AUC0-36h) for BH@MCM-41 MPs was 1.2-fold greater than for BH@MMT MPs, and significantly higher than for the BH solution and Betoptic. These findings suggest that BH@MCM-41 MPs offer enhanced efficacy for sustained glaucoma treatment through improving precorneal retention.