In-situ Fourier-transform infrared (FTIR) spectroscopy has been recognized as an important technology for online monitoring of chemical reactions. However, analysis of the real-time IR data for identification and quantification of uncertain reactants or intermediates is often ambiguous and difficult. Here we propose an analysis algorithm based on reaction kinetic modeling and the chemometric method of partial least squares (PLS) to comprehensively and quantitatively study reaction processes. Concentration profiles and apparent kinetic parameters can be simultaneously calculated from the spectral data, without the demand of complicated analysis on characteristic absorbance peaks or tedious sampling efforts for multivariate modeling. Paal-Knorr reactions and glyoxylic acid synthesis reactions were selected as typical reactions to validate the algorithm. The quantitative results were verified by measurements and demonstrated great credibility of this method. Moreover, the reaction kinetic models extracted from FTIR data were used to simulate reaction processes and optimize the conditions in order to maximize product yields. This analysis method based on kinetic modeling and the PLS method has been proven as a useful tool to quantitatively study the chemical reaction and has the ability for reaction monitoring and process optimization.