Chronic choline insufficiency reprograms hepatic metabolism and drives insulin resistance independent of obesity. While complete choline deficiency causes liver injury, the metabolic consequences of sustained, suboptimal intake, observed in ∼90% of US adults, remain poorly defined. Here, we used integrated lipidomic, metabolomic, and transcriptomic profiling to determine how graded choline intake (0.5, 1.4, or 6.3 g/kg) regulates hepatic metabolism during a control (Con) or high-fat (HF) diet-induced obesity regimen. Under Con diets, low choline intake induced a distinct metabolic state characterized by remodeled hepatic lipid architecture, particularly within triglyceride and glycerolipid species, without altering bulk triglyceride accumulation. Mechanistically, low choline disrupted phospholipid balance and induced a coordinated, sex-dependent transcriptional response, identifying ethanolamine-phosphate phospho-lyase (ETNPPL) and the fatty acid transporter CD36 as top choline-responsive genes. These metabolic effects were unique to the Con low choline group, as a high-fat diet masked all choline-dependent variations. Specifically, ETNPPL protein abundance increased under low choline Con conditions in males but not females. Functionally, this sustained restriction led to progressive hyperglycemia and insulin resistance exclusively in male mice, whereas females remained metabolically protected. Together, these findings demonstrate that chronic choline restriction remodels hepatic lipid metabolism in the absence of obesity and define a CD36–ETNPPL axis linking choline availability to sex-specific insulin resistance.