In this study, Sr(Ce0.6Zr0.4)1−xYxO3−δ (x = 0.1, 0.15, 0.2, 0.25, 0.3, SCZY) perovskite proton-conducting ceramics were synthesized using the citrate-ethylenediaminetetraacetic acid complexing method. The effect of the Y concentration on the crystal structure, electrochemical performance and hydrogen flux of the SCZY samples in air and a H2 atmosphere were investigated. The sintered SCZY samples showed a main perovskite crystal structure with several SrY2O4 impurity phases when x ≥ 0.20. The grain size of SCZY samples when x = 0.25 and 0.30 was smaller than that of other samples. The conductivity of all samples increased as the temperature increased in both air and H2; however, the conductivity of SCZY in H2 was lower than that in air. The results of AC impedance, demonstrated that resistance mainly derived from the charge transfer, which was apparently higher than the bulk and grain boundary resistance. Sr(Ce0.6Zr0.4)0.85Y0.15O3-δ exhibited low charge transfer resistance in both air and the H2 atmosphere and had a high hydrogen flux of 0.34 ml min−1 cm−2 μm−1 at 800 °C. The structures of all SCZY samples were stable in 80 °C water.