Bacterial infection commonly occurs in clinical settings when the procedure involves a medical implant. Thus, the fabrication of antimicrobial medical materials has attracted much attention in recent years. To improve the antibacterial properties of titanium (Ti)-based biomedical materials, surface microporous structures, with antimicrobial peptide coatings, were employed in this study. Native Ti substrates were endowed with a certain level of antibacterial activity after treatment with the micro-arc oxidation (MAO). A multilayer consisting of polydopamine, cationic antimicrobial peptides LL-37, and phospholipid (POPC) was coated onto MAO substrates, leading to antibacterial activity against both Gram-positive (S. aureus) and Gram-negative (E. coli) bacteria. The combination of polydopamine-LL-37-POPC was found to alleviate the burst release of LL-37 in the initial phase. This multilayer coated onto microporous Ti substrates also showed favorable cytocompatibility to both mesenchymal stem cells (MSCs) and osteoblasts. These findings illustrate a novel strategy for the development of antibacterial Ti-based implants.