A series of alkaline earth metal stannates, MSnO3 (M2+ = Ca2+, Sr2+, Ba2+), has been synthesized by a microwave hydrothermal method and subsequent heat treatment process for the first time. The obtained samples are characterized by X-ray diffraction, Brunauer-Emmett-Teller (BET) surface area analysis, UV-Vis diffuse reflectance spectroscopy, scanning electron microscopy, and a photoluminescence technique with terephthalic acid. It is found that the variation of M2+ radius in MSnO3 leads to a change in the crystal structure and the photocatalytic degradation activity for methyl orange. With the increase of M2+ radius, dipole moments are generated in octahedral units because of the octahedral tilting distortion, which may facilitate the mobility of charge carriers and improve the activities of MSnO3. The wider band gap and larger BET surface area caused by the decrease of M2+ radius also contribute to photocatalytic performances. In addition, compared with the conventional hydrothermal method, higher activity is achieved on the samples prepared by means of the microwave method. Our findings may provide insights in fabrication of highly efficient photocatalysts by adjusting the counter-cation radius.