Analysis is performed of the spectral structure of the atmosphericwaves (i. e.,harmonic spectrum along the latitudinal circle and frequency spec-trum in the time domain)simulated by the general circulation model (GCM),pro-posed by the Institute of Atmospheric Physics (IAP),Academia Sinica, and theiranomalies in an El Niño year. Results show that ultra-long waves represent theprincipal form of low-latitude waves, characterized remarkably by quasi-40-day oscillations in a given geographic locality and somewhat related to the obser-vations and significant anomalies are experienced in an El Niño year. Perhaps thepresent study is a useful attempt at the assessment of the GCM’S performancesand the expansion of its research domain.