In order to separate the chromatogram peaks and spectra from the High Performance Liquid Chromatography with Diode Array Detector (HPLC-DAD) data set, a separation model of Generalized Reference Curve Measurement and its solution by multitarget Bare Bones Particle Swarm Optimization (GRCMmBBPSO) is proposed in this paper. Firstly, parameters are constructed which will generate Reference Curves (RCs) for chromatogram peaks. Secondly, the GRCM model is proposed to transform all these parameters to scalar values, which indicate the possibility for the HPLC-DAD data set containing chromatogram peaks similar to the RCs constructed by corresponding parameters. Then, the algorithm of mBBPSO is introduced to calculate the optimal parameters by minimizing the scalar values. Finally, the spectra are estimated. Through simulations and experiments, following conclusions are drawn: (1) the GRCMmBBPSO method can extract chromatogram peaks from the simulation data set without knowing the number of the compounds in advance even when a severe overlap and white noise exist; (2) the GRCMmBBPSO method can be applied to real HPLC-DAD data set.