The automation of dynamic ultrasonic-assisted extraction (DUAE) coupled with paralleled counter-current chromatography (PCCC) was developed and used in the continuous extraction and online isolation of chemical constituents from Garcinia mangostana. The two-phase solvent system was prepared using automated equipment. The target compounds were extracted continuously by DUAE; after extraction, the extracted solution was pumped into a flash chromatographic column (FCC) for enrichment and purification. After enrichment and purification, the sample was eluted with the upper organic phase of the two-phase solvent system; the eluted solution was pumped into the CCC 1 column, and then the target compounds were eluted with the lower aqueous phase of the two-phase solvent system. During the CCC separation, the sample was continuously enriched and purified by the FCC, and the ten-port valve was switched to connect ports 1 and 2, followed by elution with the upper organic phase of the two-phase solvent system. The eluted solution was pumped into the CCC 2 column, and then the target compounds were eluted with the lower aqueous phase of the two-phase solvent system. When the first cycle of DUAE/PCCC was complete, the second cycle was performed. Five target compounds, i.e., 3-isomangostin, 8-desoxygartanin, mangostanol, gartanin, and α-mangostin, with purities above 94.28%, were successfully extracted and isolated online via a two-phase solvent system consisting of n-hexane–ethyl acetate–acetonitrile–methanol–water (5:2:5:1:3, v:v:v:v:v). This instrumental setup achieved systematic extraction and isolation of natural products, and has great prospects for industrial applications.