Choline is essential for infant development. Human milk choline is predominately present in three water-soluble choline (WSC) forms: free choline (FC), phosphocholine (PhosC), and glycerophosphocholine (GPC). It is unclear whether mother’s own preterm milk and pooled donor milk differ in WSC composition and whether WSC compounds are interrelated. Mother’s own preterm milk (n = 75) and donor milk (n = 30) samples from the neonatal intensive care unit, BC Women’s Hospital were analyzed for WSC composition using liquid chromatography tandem mass spectrometry (LC-MS/MS). Associations between different WSC compounds were determined using Pearson’s correlations, followed by Fischer r-to-z transformation. Total WSC concentration and concentrations of FC, PhosC, and GPC did not significantly differ between mother’s own milk and donor milk. FC was negatively associated with PhosC and GPC in mother’s own milk (r = −0.27, p = 0.02; r = −0.34, p = 0.003, respectively), but not in donor milk (r = 0.26, p = 0.181 r = 0.37, p = 0.062, respectively). The difference in these associations between the two milk groups were statistically significant (p = 0.03 for the association between PhosC and FC; and p = 0.003 for the association between FC and GPC). PhosC and GPC were positively associated in mother’s own milk (r = 0.32, p = 0.036) but not donor milk (r = 0.36, p = 0.062), although the difference in correlation was not statistically significant. The metabolic and clinical implications of these associations on the preterm infant need to be further elucidated.