The effects of laser pulse duration and polarization on the femtosecond filament-induced fluorescence of combustion intermediates were studied herein. The variations in the fluorescence spectra of combustion intermediates, such as OH, CH, CN, C₂, and C, were observed by varying laser pulse duration and polarization. The results show that the fluorescence intensities of all the observed combustion intermediates decrease with the increase of laser pulse duration and polarization ellipticity. This behavior is explained by the fact the clamped intensities and plasma densities inside the filament core are strongly dependent on laser pulse duration and polarization, leading to the changes in the multiphoton-excited signals of combustion intermediates.