Spectral measurements of complex heterogeneous types of mixture samples are often affected by significant multiplicative effects resulting from light scattering, due to physical variations (e.g., particle size and shape, sample packing, and sample surface, etc.) inherent within the individual samples. Therefore, the separation of the spectral contributions due to variations in chemical compositions from those caused by physical variations is crucial to accurate quantitative spectroscopic analysis of heterogeneous samples. In this work, an improved strategy has been proposed to estimate the multiplicative parameters accounting for multiplicative effects in each measured spectrum and, hence, mitigate the detrimental influence of multiplicative effects on the quantitative spectroscopic analysis of heterogeneous samples. The basic assumption of the proposed method is that light scattering due to physical variations has the same effects on the spectral contributions of each of the spectroscopically active chemical components in the same sample mixture. On the basis of this underlying assumption, the proposed method realizes the efficient estimation of the multiplicative parameters by solving a simple quadratic programming problem. The performance of the proposed method has been tested on two publicly available benchmark data sets (i.e., near-infrared total diffuse transmittance spectra of four-component suspension samples and near-infrared spectral data of meat samples) and compared with some empirical approaches designed for the same purpose. It was found that the proposed method provided appreciable improvement in quantitative spectroscopic analysis of heterogeneous mixture samples. The study indicates that accurate quantitative spectroscopic analysis of heterogeneous mixture samples can be achieved through the combination of spectroscopic techniques with smart modeling methodology.