The light-harvesting chlorophyll a/b complex of photosystem II (LHCII) is able to switch to multiple functions under different light conditions (i.e. harvesting solar energy for photosynthesis and dissipating excess excitation energy for photoprotection). The role of the different carotenoids bound to LHCII in regulating the structure and function of the complex is a long-lasting question in photosynthesis research. 9-cis-Neoxanthin (Nx) is one of the important carotenoids, which can only be found in the LHCIIs. High-resolution structural analysis of LHCII shows that Nx is located between different monomeric LHCIIs, with one side protruding into the lipid membrane. In this study, the various functional significances of this unique feature of Nx binding in LHCII are studied with the in vitro reconstituted LHCIIs both with and without Nx and the native complexes isolated either from wild-type Arabidopsis (Arabidopsis thaliana) or from its mutant aba4-3 lacking Nx. Our results reveal that the binding of Nx affects the binding affinity of violaxanthin (Vx) to LHCII significantly. In the absence of Nx, Vx has a much higher binding affinity to trimeric LHCII. The strong coordination between Nx and Vx at the interfaces of adjacent monomers of LHCII plays an important role both in operating the xanthophyll cycle and in the transient modulation of nonphotochemical quenching.