It is synthesized that the CdS and CdSe quantum dots with the different sizes in the organic phase. The CdS and CdSe quantum dots were assembled into multi-layer composite nanostructures using LB technology. We also investigate the fluorescence resonance energy transfer (FRET) of the quantum dots system and the multi-layer nanostructures. The results reveal that the fluorescence intensity of CdS quantum dots comparatively weaken seriously with the complete volatilization of solvents in CdS and CdSe quantum dots hybrid solution. This results in the enhancing of the FRET rate as minishing the intervals of quantum dots. In multi-layer composite nanostructures, the fluorescence intensity of CdSe quantum dots layer en- hances with increasing the layer number of CdS quantum dots. This shows the increase of FRET rate with adding donor layers.