Five main components of Azolla imbricata were isolated and identified as caffeoylquinic acid derivatives, four of which were isolated from this species for the first time. The five compounds exhibited strong antioxidant activities and were used as chemical markers for quantitative analysis. A chitosan-based matrix solid-phase dispersion (MSPD) extraction coupled with high-performance liquid chromatography (HPLC) was developed for the determination of the five analytes in A. imbricata. The optimal conditions for the chitosan-based MSPD extraction were as follows: low viscosity chitosan HL-1 as the dispersant, sample-to-dispersant mass ratio of 1:1, 10 mL of a methanol-sulfuric acid aqueous solution (0.2 M) (7:3, v/v) as the elution solvent, and a grinding time of 1 min. Compared with ultrasonic assisted extraction (UAE), the chitosan-based MSPD extraction exhibited higher extraction efficiency, consumed less solvent and time, and provided a cleaner extract. Compared with C18-based MSPD, the developed method was less expensive and more environmentally-friendly. The validated MSPD–HPLC method was efficient, reliable, and applicable to the quantification of caffeoylquinic acids in A. imbricata.