Utilizing machine learning techniques for data-driven diagnosis of high temperature PEM fuel cells is beneficial and meaningful to the system durability. Nevertheless, ensuring the robustness of diagnosis remains a critical and challenging task in real application. To enhance the robustness of diagnosis and achieve a more thorough evaluation of diagnostic performance, a robust diagnostic procedure based on electrochemical impedance spectroscopy (EIS) and a new method for evaluation of the diagnosis robustness was proposed and investigated in this work. To improve the diagnosis robustness: (1) the degradation mechanism of different faults in the high temperature PEM fuel cell was first analyzed via the distribution of relaxation time of EIS to determine the equivalent circuit model (ECM) with better interpretability, simplicity and accuracy; (2) the feature extraction was implemented on the identified parameters of the ECM and extra attention was paid to distinguishing between the long-term normal degradation and other faults; (3) a Siamese Network was adopted to get features with higher robustness in a new embedding. The diagnosis was conducted using 6 classic classification algorithms—support vector machine (SVM), K-nearest neighbor (KNN), logistic regression (LR), decision tree (DT), random forest (RF), and Naive Bayes employing a dataset comprising a total of 1935 collected EIS. To evaluate the robustness of trained models: (1) different levels of errors were added to the features for performance evaluation; (2) a robustness coefficient (Roubust_C) was defined for a quantified and explicit evaluation of the diagnosis robustness. The diagnostic models employing the proposed feature extraction method can not only achieve the higher performance of around 100% but also higher robustness for diagnosis models. Despite the initial performance being similar, the KNN demonstrated a superior robustness after feature selection and re-embedding by triplet-loss method, which suggests the necessity of robustness evaluation for the machine learning models and the effectiveness of the defined robustness coefficient. This work hopes to give new insights to the robust diagnosis of high temperature PEM fuel cells and more comprehensive performance evaluation of the data-driven method for diagnostic application.