In an iodine-cell-based Rayleigh Doppler lidar (RDLD), slow drift in the relative spectral position between the transmitted laser frequency and the discriminator response can shift the zero-Doppler reference and introduce systematic wind errors. This study proposes and validates an online zero-Doppler reference tracking and wind correction method based on time-division multiplexed measurements of seed reference light. The seed reference light and atmospheric backscatter share a single iodine-cell frequency discriminator, and the seed transmittance is used to determine the spectral position of the emitted laser relative to the current discriminator response and update the zero-Doppler reference online. In a dynamic frequency-tracking experiment, the difference between Doppler frequency-discrimination receiver (DFDR) and wavemeter measurements had a standard deviation of 1.25 MHz. During the 8 h continuous measurement, hour-scale variations of several megahertz were observed in the relative spectral position, indicating that the zero-Doppler reference may not remain strictly constant during long-term operation. With integration times of 100–1000 s, the Allan deviation of the frequency measurements was reduced to approximately 0.29 MHz. The frequency difference between the seed reference light and pulsed laser had a standard deviation of 1.14 MHz, supporting the use of the seed reference light to track pulsed-laser frequency variations. In atmospheric observations, the mean vertical wind speed shifted from approximately 1.2 to −0.34 m s⁻¹ after zero-Doppler reference correction. In a controlled frequency-offset experiment, RDLD retrieved equivalent wind speeds agreed well with values derived from independent wavemeter measurements. Measured zonal and meridional winds also agreed well with ERA5 reanalysis in their major vertical structures and temporal evolution. These results demonstrate that the method enables online monitoring and correction of the RDLD zero-Doppler reference without continuous reliance on an external wavemeter, improving the stability of long-term wind measurements.