When LHCII forms aggregates, the internal conformational changes will result in chlorophyll fluorescence quenching. Uncovering the molecular mechanism of this phenomenon will help us to understand how plants dissipate the excess excitation energy through non-photochemical quenching (NPQ) process. The crystal structure of spinach and pea LHCII have been published, and recently, we solved another crystal structure of LHCII from cucumber at 2.66A resolution. Here we present the first direct structural evidence indicating that the two lutein(Lut) molecules bound in each LHCII monomer have different conformations, Lut621 has a more twisted conformation than that of Lut620. The intimate interaction between the Lut620 and Chla612/Chla611 dimer leads to form a hetero-trimer, which is considered to be a potential quenching site. We also discovered that the dehydration of the LHCII crystals resulted in a notable shrinkage of the crystal unit cell dimensions which was accompanied by a red-shift of the fluorescence emission spectra of the crystals. These phenomena suggest the changes in the crystal packing during dehydration might be the cause of internal conformational changes within LHCII. We proposed a conformational change related NPQ model based on the structure analysis.