Increasing evidence supports the existence of fetal-originated adult diseases. Recent research indicates that the intrauterine environment affects the fetal hypothalamic energy intake center. Inulin is a probiotic that can moderate metabolic disorders, but whether maternal inulin intervention confers long-term metabolic benefits to lipid metabolism in offspring in their adult lives and the mechanism involved are unknown. Here, we used a maternal overnutrition model that was induced by excess energy intake before and during pregnancy and lactation and maternal inulin intervention was performed during pregnancy and lactation. The hypothalamic genome methylation in offspring was analyzed using a methylation array. The results showed that maternal inulin treatment modified the maternal high-fat diet (HFD)-induced increases in body weight, adipose tissue weight, and serum insulin and leptin levels and decreases in serum adiponectin levels. Maternal inulin intervention regulated the impairments in hypothalamic leptin resistance, induced the methylation of Socs3, Npy, and Il6, and inhibited the methylation of Lepr in the hypothalamus of offspring. In conclusion, maternal inulin intervention modifies offspring lipid metabolism, and the underlying mechanism involves the methylation of genes in the hypothalamus feeding circuit.