The stability of catalytic membrane reactors (CMRs) is crucial for the practical applications in chemical reaction processes. However, currently reported CMRs with perovskite-based oxygen permeable membranes usually show poor stability owing to the over-reduction of Co and Fe ions in perovskite lattice under harsh reducing gas atmospheres and the interaction between membrane and catalyst. Here we developed an oxygen permeable membrane Ce0.9Gd0.1O2-δ-SrCe0.5Fe0.5O3-δ (CGO-SCF) with Ce0.9Gd0.1O2-δ (CGO) protective layer to construct a catalytic membrane reactor packed with Ni/Al2O3 catalyst for partial oxidation of methane. The CGO dense protective layer can effectively avoid the over-reduction of Fe ions in perovskite under harsh reducing gas atmospheres and the interaction between perovskite and Ni/Al2O3. Benefiting from high stability and mixed ionic-electronic conductivity of CGO in a low oxygen partial pressure environment, the developed membrane reactor with a dense CGO thin film was successfully operated with a stable CH4 conversion of 87% and a H2/CO ratio of 2 over 200 h in harsh operating conditions. This strategy proposed here provides insights into the design of highly stable catalytic membrane reactor in harsh conditions.