Human milk is an intricate, bioactive food promoting infant health. We studied the composition of human milk samples collected over an 8-month lactation using ¹H NMR metabolomics. A total of 72 human breast milk samples were collected from ten Chinese mothers at eight different time points. The concentrations of ten human milk oligosaccharides (HMOs), fucose and lactose were quantified. Six of the mothers were classified as Lewis-positive secretors (Se⁺Le⁺) and four as Lewis-positive non-secretors (Se⁻Le⁺) based on the levels of 2′-fucosyllactose (2′-FL), lacto-N-fucopentaose (LNFP) II, lactodifucotetraose (LDFT) and lacto-N-neotetraose (LNnT). Acetate, citrate, short/medium-chain fatty acids, glutamine and urea showed a time-dependent trend in relation to the stage of lactation. The concentrations of 2′-FL, 3-FL (3-fucosyllactose), 3′-SL (3′-sialyllactose), LDFT, LNFP I, LNFP II, LNFP III, LNnT, LNT (lacto-N-tetraose), and fucose were statistically different between secretors and non-secretors. A temporal difference of approximately 1–2 months between the development of non-secretor and secretor HMO profiles was shown. The results highlighted the importance of long-term breastfeeding, especially among non-secretors.