Three fractions (I–III) were separated from crude oligosaccharides of lotus seeds by fast protein liquid chromatography with final purity of 97.6, 96.3, and 96.8%, respectively. The fractions were identified as sucrose, raffinose, and stachyose by using TLC, HPLC with charged aerosol detector (CAD), LC-MS, and methylation analysis. Subsequently sucrose and raffinose family oligosaccharides (RFOs) with degree of polymerization (DP) 3–5 (raffinose, stachyose, and verbascose) have been quantified by HPLC-CAD for the first time. All calibration curves for investigated analytes showed good linear regression (R > 0.9952). Their limit of detection and limit of quantity were in the ranges 0.14−0.28 and 0.36−0.48 μg/mL, respectively. The recoveries ranged from 96.6 to 103.4%. The contents of sucrose and RFOs DP3–DP5 were different in lotus seeds and other parts of lotus samples, but similar in their own variety. Additionally, the distribution of RFOs in different parts of lotus were also compared and the results indicated that RFOs might be mainly synthesized in lotus seeds. This work is helpful for understanding the way of biosynthesis of RFOs in lotus as well as quality control of plants containing RFOs.