Measurements of Very Low Frequency (VLF) signals from navy transmitters carry direct information about the D‐region ionosphere and have been widely utilized for detecting the electron density at D‐region altitudes, but not frequently for the atmospheric waves therein. Atmospheric waves have been extensively studied using the total ionospheric electron content, but if and how they are correlated with the D‐region ionosphere and VLF measurements still remains poorly investigated. In this study, we have conducted a comprehensive analysis using 7‐year measurements (2016–2022) of VLF signals from the JJI, NWC, and VTX transmitters as being recorded in Suizhou, China. These three transmitter‐receiver paths are representative and the corresponding observations constitute a valuable data set to investigate the periodicities of VLF data. Different from previous studies, we have utilized the ensemble empirical mode decomposition and Lomb‐Scargle methods to determine the periodicities of these data. By contrasting these paths, prominent periodicities ranging from 2 to 730 days have been found, with clear diurnal variation and suggestive latitudinal/longitudinal dependence. Moreover, we have found that the mesospheric temperature is closely related with the annual oscillation of VLF measurements, while this oscillation has a low correlation with solar Lyman‐α fluxes or geomagnetic activity. The oscillations with relatively shorter periods are likely atmospheric waves such as gravity waves, planetary waves, or harmonics of these waves. Our results suggest that, in addition to the electron density, the subionospheric VLF technique can be potentially utilized to remotely sense atmospheric waves that propagate up to or through the D‐region ionosphere.