Carrageenans are widely utilized in many commercial applications such as the food and pharmaceutical industry, due to their excellent functional properties. In this study, a sensitive LC-MS/MS method was developed to determine κ-3, κ-5, and κ-7 carrageenan oligosaccharides simultaneously. Optimum MRM transitions for κ-3, κ-5, and κ-7 carrageenan oligosaccharides were (645.079→565.111, [M-H] −), (515.137→474.946, [M-2H] 2−), and (471.484→445, [M-3H] 3−), respectively. Chromatographic separation was performed on an Amide column coupled with a guard column operated at 60°C under stepwise gradient elution. The linearity of the LC-MS/MS method for κ-3, κ-5, and κ-7 carrageenan oligosaccharides, evaluated over the concentration range of 0.10–20.0 μmol L −1, was excellent. The precisions of the method for κ-3, κ-5, and κ-7 carrageenan oligosaccharides were from 0.91% to 9.66%, and the inter-day precisions were from 0.92% to 10.5%. Validation of the LC-MS/MS method indicated that the method was precise and in line with the CFDA guidance. This method has been successfully applied to an in vitro absorption study.