Fault detection in the landing gear retraction/extension hydraulic system is difficult due to uncertainties in component parameters and sensor measurement values. This work lies in the introduction of linear fractional transformation technology and uncertainty analysis theory for the construction of the diagnostic bond graph of the landing gear retraction/extension hydraulic system. Thus, interval analytical redundancy relations can be derived as well as fault signature matrices. By using the fault signature matrix, existing faults can be detected and isolated preliminary. Furthermore, interval analytical redundancy relations can be used to detect system faults in detail. The analysis results of the failure cases of the internal and external leakage of the actuator and landing gear selector valve reversing stuck show that compared to the traditional analytical redundancy relations, this method takes into account the negative factors of uncertainty, so it can effectively reduce missed diagnosis and misdiagnosis; compared to the traditional absolute diagnostic threshold, the interval diagnostic threshold is more accurate and sensitive.