This paper investigates over-the-air computation (AirComp) in the context of multiple-access time-varying multipath channels. We focus on a scenario where devices with high mobility transmit their sensing data to a fusion center (FC) for averaging. To combat the time-varying channel and Doppler effect, each device adopts orthogonal time frequency space (OTFS) modulation. After signals are received by the FC, the aggregated data undergoes demodulation and estimation within the delay-Doppler domain. We leverage the mean squared error (MSE) as a metric for the computational error of OTFS-based AirComp. We then derive the optimal transmit power at each device and signal scaling factor at FC for minimizing MSE. Notably, the performance of OTFS-based AirComp is not only affected by the noise but also by the inter-symbol interference and inter-link interference arising from the multipath channel. To counteract the interference-induced computational errors, we incorporate zero-padding (ZP)-assisted OTFS into AirComp and propose algorithms for interference cancellation. Numerical results underscore the enhanced performance of ZP-assisted OTFS-based AirComp over naive OTFS-based AirComp.