The aircraft environmental control system (ECS) is a critical aircraft system, which provides the appropriate environmental conditions to ensure the safe transport of air passengers and equipment. The functionality and reliability of ECS have received increasing attention in recent years. The heat exchanger is a particularly significant component of the ECS, because its failure decreases the system's efficiency, which can lead to catastrophic consequences. Fault diagnosis of the heat exchanger is necessary to prevent risks. However, two problems hinder the implementation of the heat exchanger fault diagnosis in practice. First, the actual measured parameter of the heat exchanger cannot effectively reflect the fault occurrence, whereas the heat exchanger faults are usually depicted by utilizing the corresponding fault-related state parameters that cannot be measured directly. Second, both the traditional Extended Kalman Filter (EKF) and the EKF-based Double Model Filter have certain disadvantages, such as sensitivity to modeling errors and difficulties in selection of initialization values. To solve the aforementioned problems, this paper presents a fault-related parameter adaptive estimation method based on strong tracking filter (STF) and Modified Bayes classification algorithm for fault detection and failure mode classification of the heat exchanger, respectively. Heat exchanger fault simulation is conducted to generate fault data, through which the proposed methods are validated. The results demonstrate that the proposed methods are capable of providing accurate, stable, and rapid fault diagnosis of the heat exchanger.