This correspondence presents a new decentralized nonlinear adaptive controller (DNAC) for a heating, ventilating, and air conditioning (HVAC) system capable of maintaining comfortable conditions under varying thermal loads. In this scheme, an HVAC system is considered to be two subsystems and controlled independently. The interactions between the two subsystems are treated as deterministic types of uncertain disturbances and their magnitudes are supposed to be bounded by absolute value. The decentralized nonlinear adaptive controller (DNAC) consists of an inner loop and an outer loop. The inner loop is a single-input fuzzy logic controller (FLC), which is used as the feedback controller to overcome random instant disturbances. The outer loop is a Fourier integral-based control, which is used as the frequency-domain adaptive compensator to overcome steady, lasting uncertain disturbances. The global DNAC controller ensures that the system output vector tracks a desired trajectory vector within the system bandwidth and that the tracking error vector converges uniformly to a zero vector. The simulated experimental results on the HVAC system show that the performance is dramatically improved.