Previous studies have shown that Foxc1 and Foxc2, closely related Fox transcription factors, have interactive roles in cardiovascular development. However, little is known about their functional overlap during early heart morphogenesis. Here, we show that Foxc genes are coexpressed in a novel heart field, the second heart field, as well as the cardiac neural crest cells (NCCs), endocardium, and proepicardium. Notably, compound Foxc1; Foxc2 mutants have a wide spectrum of cardiac abnormalities, including hypoplasia or lack of the outflow tract (OFT) and right ventricle as well as the inflow tract, dysplasia of the OFT and atrioventricular cushions, and abnormal formation of the epicardium, in a dose-dependent manner. Most importantly, in the second heart field, compound mutants exhibit significant downregulation of Tbx1 and Fgf8/10 and a reduction in cell proliferation. Moreover, NCCs in compound mutants show extensive apoptosis during migration, leading to a failure of the OFT septation. Taken together, our results demonstrate that Foxc1 and Foxc2 play pivotal roles in the early processes of heart development, especially acting upstream of the Tbx1-FGF cascade during the morphogenesis of the OFT.