BACKGROUND: Acellular tubular artery scaffolds offer structural support for vascular regeneration but are inherently limited by poor anticoagulant properties, which increases the risk of thrombus formation following implantation. This thrombogenicity remains a major obstacle to their clinical application, particularly in small-diameter vascular grafts. METHODS: To address this challenge, the present study investigates the use of the Layer-by-Layer (LbL) assembly technique for heparin immobilization under low-speed rotation. Utilizing a roller tube system, heparin was immobilized onto decellularized scaffolds through electrostatic interactions facilitated by a DHI-based linker. This low-speed rotation LbL approach enhanced the uniformity and stability of heparin deposition compared to traditional static methods. One, 4, 7, 10, 13 deposition cycles were performed to achieve optimal heparin loading, resulting in scaffolds capable of sustained heparin release over 28 days. RESULTS: The heparinized scaffolds exhibited an initial burst release (approximately 80%), followed by a sustained phase with 18.24% ± 0.242 remaining to support prolonged anticoagulant activity. Importantly, the modified scaffolds significantly reduced thrombus formation and exhibited minimal hemolytic activity, indicating improved hemocompatibility. In addition to their antithrombotic properties, the scaffolds also promoted endothelial cell adhesion, which is critical for restoring vascular integrity, regulating vascular tone, and maintaining long-term patency. CONCLUSION These findings highlight the efficacy of roller-assisted LbL heparinization as a practical and scalable strategy to enhance the blood compatibility of acellular vascular grafts. This method holds considerable promise for addressing thrombogenicity in vascular tissue engineering and advancing the clinical translation of bioengineered vascular constructs.