An efficient enantioselective Mannich reaction of imines bearing a heterocycle with malonates catalysed by a cinchona-based squaramide organocatalyst has been developed. This catalytic asymmetric reaction afforded the β-amino ester derivatives containing a heterocycle moiety in high yields (up to 99%) and excellent enantioselectivities (up to 98%) in most cases. The imines with an electron-withdrawing group afforded the adducts with better yields than those bearing an electron-donating group in this reaction.