A new concept of optical encoding approach, surface enhanced Raman scattering (SERS)-fluorescence joint spectral encoding method (SFJSE), was demonstrated by using organic-metal-quantum dot (QD) hybrid nanoparticles (OMQ NPs) with a nanolayered structure. This method has two distinct characteristics, which make it more feasible to achieve enormous codes in practice, compared with a sole fluorescence- or SERS-based encoding protocol. One of the two characteristics is to use the joint SERS and fluorescence spectra as the encoding elements instead of an individual optical signal, resulting in a broadened optical spectrum range for efficient encoding. The other is to assemble SERS reporters and fluorescent agents onto different layers of OMQ NPs, leading to an easier fabrication protocol when a large number of agents need to be involved into encoding carriers. By conjugating different antibodies to OMQ NPs with varied codes, the potential application of such an encoding system in high-throughput detection has been investigated by multiplex sandwich immunoassays. The high specificity and sensitivity of the assays suggest that the SFJSE method could be developed as a powerful encoding tool for high-throughput bioanalysis with the use of OMQ NPs.