In this work, we have developed green and efficient regioselective and chemoselective syntheses of 5‐aryloyl‐1,3‐dimethyl‐7‐thioxo‐5,6,7,8‐tetrahydropyrimido[4,5‐d]pyrimidine‐2,4(1H,3H)‐dione and 5‐aryloyl‐1,3‐dimethyl‐2,7‐dithioxo‐2,3,5,6,7,8‐hexahydropyrimido[4,5‐d]pyrimidin‐4(1H)‐one derivatives via one‐pot three‐component Biginelli‐like condensation of arylglyoxal monohydrates, N,N‐dimethylbarbituric acid or N,N‐dimethyl‐2‐thiobarbituric acid, and thiourea in water at 50°C. The presence of two different green catalytic systems (ZrOCl2.8H2O and also DABCO) proceeded efficiently to afford the desired products in good‐to‐excellent yields. An aqueous reaction medium, high regioselectivity and chemoselectivity, simple operation and suitable yields of products are the important features of these green protocols.