Atherosclerosis (AS), a chronic inflammatory vascular disease, is a major cause of cardiovascular morbidity and mortality worldwide. Indigo naturalis (IN) is a medicinal and edible plant with obvious pharmacological effects such as anti-inflammation, improving blood circulation, and antibacterial. However, its therapeutic efficacy and mechanism of action against AS remain unclear. This study aims to integrate network pharmacology, molecular docking, and in vitro and in vitro experimental evaluations to uncover the active components and multitarget mechanisms of IN against AS. 10 active ingredients and 96 related target genes were identified, and gene functional enrichment analysis suggested that the toll-like receptor signaling pathway plays a core role in IN’s action against AS. Molecular docking revealed strong binding affinities between IN’s key ingredients and hub genes. In vitro, IN regulated the expression of inflammatory factors, migration factors, and TLR4, NF-κB, and MyD88 proteins in cell inflammation models as predicted. In vivo, IN reduced aorta damage, cell apoptosis, blood lipids level, and inflammatory factors in LPS-induced AS mice, further downregulating the expression levels of TLR4, NF-κB, and MyD88. This study confirmed the feasibility of IN for AS treatment from an anti-inflammatory perspective, highlighting the TLR4/MyD88/NF-κB pathway as a critical mechanism. These findings provide a basis for developing IN as a potential candidate for anti-AS clinical application.