We report on an experimental investigation on the dynamic decoherence process of molecular rotational wavepackets during femtosecond laser filamentation based on time-dependent mean wavelength shifts of a weak probe pulse. Details of periodic revival structures of transient alignment can be readily obtained from the measured shifted spectra due to the periodic modulation of the molecular refractive index. Using the method, we measured decoherence lifetimes of molecular rotational wavepackets in ${\mathrm{N}}_2$ and ${\mathrm{O}}_2$ under different experimental conditions. Our results indicate that decoherence lifetimes of molecular rotational wavepackets are primarily determined by the relative population of rotational states in the wave packet and intermolecular collisions, rather than the focusing intensity.