Laser-induced breakdown spectroscopy (LIBS) is an atomic emission spectrometry technique for material component analysis. However, the spectral signal distortion and the low analytical accuracy remain as challenges due to the self-absorption effect of atomic lines in LIBS. Here, to overcome this flaw, we demonstrated a method to build calibration with molecular emission, which was measured from a mixture of H₃BO₃ and C₆H₁₂O₆·H₂O in powder form. We compared the calibration established by typical atomic emission and molecular emission of boron monoxide. The results showed that the self-absorption effect and R² values were improved by using molecular spectra. Furthermore, to improve the accuracy of molecular emission content determination, a genetic algorithm and partial least squares regression (GA-PLSR) combination model was adopted. The achieved root mean square error of prediction (RMSEP) and the mean prediction error (MPE) for the GA-PLSR model were 0.8667 wt% and 10.9685%, respectively. The results demonstrated that it is a potential method to overcome the self-absorption effect with molecular emission and the accuracy of boron content determination of molecular emission can be improved with the GA-PLSR model.