Stress relaxation probing on the immiscible blends is an attractive route to reveal the time-dependent morphology-viscoelasticity correlations under/after flow. However, a comprehensive understanding on the stress relaxation of co-continuous blends, especially after subjected to a shear strain, is still lacking. In this work, the stress relaxation behavior of co-continuous polystyrene/poly(methyl methacrylate) (50/50) blends with different annealing times, strain levels, and temperatures was examined under step shear strain and was correlated with the development of their morphologies. It was found that co-continuous blends display a fast relaxation process which corresponded to the relaxation of bulk polymer and a second slower relaxation process due to the recovery of co-continuous morphology. The stress relaxation rates of co-continuous blends tend to decrease due to the coarsening of instable co-continuous structure during annealing. Furthermore, the stress relaxation of the co-continuous blends is strongly affected by the change of viscosity and interfacial tension caused by the temperature. The contribution of morphological coarsening, viscosity, and interfacial tension variation on the stress relaxation behavior of co-continuous blends was discussed based on the Lee-Park model and time-temperature superposition principle, respectively.