We have developed a new wave scheme particularly aiming to provide better temperature fields with realistic variability for trajectory modeling of dehydration processes in the tropical tropopause layer (TTL). The new scheme includes amplitude-phase interpolation and amplification of waves in reanalysis data. Amplification factors are based on statistical variability differences between reanalysis data and radiosonde observations at 24 tropical locations during 1997–2013 boreal winters. We show that conventional linear interpolation of temperatures in the vertical coordinate degrades wave amplitudes and variability. Amplitude-phase interpolation in Fourier space greatly mitigates the problem found in linear interpolation. Furthermore, amplitudes of existing waves in reanalyses were amplified to generate realistic variability. In addition to improvements in variability, the scheme lowers cold point temperatures and raises cold point tropopause heights. Having realistic variability with the new approach will reduce uncertainties in simulations of TTL cirrus clouds and stratospheric water vapor.