Dietary consumption of flavonoids correlated positively with lower risk of cardiovascular disease. However, the precise roles of flavonoids from the blossoms of Citrus aurantium Linn variant amara Engl (CAVA) in atherosclerosis (AS) are still poorly understood. This study aimed to find novel flavonoid-type skeletons with protection against AS. Total flavonoids (CAVAF), homoeriodictyol (HE) and hesperetin-7-O-beta-d-glucopyranoside (HG) were isolated from the blossoms of Citrus aurantium Linn variant amara Engl. by chromatography. Their suppressive effects on lipopolysaccharide (LPS)-induced inflammatory responses and ox-LDL-induced foam cell formation were systematically and comparatively investigated using macrophage RAW264.7 cells. HE was more powerful than HG in inhibiting LPS-induced production of nitric oxide (NO), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-alpha), interleukin-1 beta (IL-1 beta) and gene expression in RAW264.7 cells. HE and HG showed different responses to extracellular signal-regulated kinases (ERK), c-Jun N-terminal kinases (JNK), P38, P65, I kappa B alpha, I kappa K alpha/beta phosphorylation, and nuclear factor-kappa B (NF-kappa B) nuclear translocation. HE and HG also differentially decreased oxidized low-density lipoprotein (ox-LDL)-induced foam cell formation by regulating peroxisome proliferator-activated receptor-gamma (PPAR gamma), phospholipid ATP-binding cassette transporter A1 (ABCA1), phospholipid ATP-binding cassette transporter G1 (ABCG1), scavenger receptor class B type I (SRB1), scavenger receptor class A type I (SRA1) and cluster of differentiation 36 (CD36) expression at gene and protein levels in RAW264.7 cells. HG showed weaker potential than HE in preventing AS development. Their chemical differences might partially explain the discrepancy in their bioactivity. In conclusion, HE and HG might be developed into novel therapeutic agents against inflammation and AS-associated diseases.