A novel synergistic effect during supramolecular host-guest encapsulations of core-shell amphiphilic hyperbranched polymers to two kinds of dyes was reported. Two kinds of palmityl chloride-modified hyperbranched polymer, polyamidoamine (HPAMAM10K-C16) and poly(sulfone-amine) (HPSA11K-C16), were used as the hosts of supramolecular encapsulations, and water-soluble dyes such as methyl orange (MO) and methyl blue (MB) were selected as the corresponding guests. In cases of single-dye encapsulations, each host can extract one kind of guest from water phase into chloroform phase with a certain loading capacity (C-load). In the double-dye encapsulations, a pair of dyes, MO and MB, was employed as the guests. The C-load increased significantly for one or both of the pair dyes with the C-load of the single-dye encapsulation as the reference. This is defined as synergistic encapsulation in this paper. For the HPAMAM10K-C16, C-load of MO can be increased by about 100% with the cooperation of MB. For HPSA11K-C16, C-load of MB can be raised to a 40-100-fold level of single-dye encapsulation without loss of MO. Experiments with different encapsulating sequence showed that the synergistic encapsulation for HPAMAM10K-C16 is a parallel-type process because the sequence has no significant impact on the C-load of each dye, while the case of HPSA11K-C16 is a cascade-type process since the results with different encapsulating order were different. The synergistic encapsulation phenomenon was confirmed by the measurements of H-1 NMR, DSC, and TGA on the resulting dye-encapsulated hyperbranched polymers. In addition, investigations on the guest-host supramolecular systems with different pH indicated that the pH value has certain influence on the synergistic encapsulation C-load, but it was not the dominating factor for the synergistic encapsulation. The synergistic effect was found simultaneously in the supramolecular encapsulation of two hosts, indicating this effect is not limited to a peculiar dendritic polymer. The phenomenon presented here will trigger further application of dendritic and other complex polymeric materials in the supramolecular host-guest chemistry.