A new robust fault diagnosis method based on linear matrix inequality (LMI) for non-linear difference-algebraic systems (DAS) with uncertainties is proposed. Based on the known nominal model of DAS, it firstly constructs an auxiliary system consisting of a difference equation and an algebraic equation, then converts the problem of fault identification into the problem of parameter estimation, and finally realizes fault identification using an LMI method. This method can not only detect, isolate and identify faults for DAS, but also give the upper bounds of fault identification error. Simulation indicates that it can give satisfactory diagnostic results for both abrupt and incipient faults.