Bright- and black-blood MRI sequences provide complementary diagnostic information in patients with congenital heart disease (CHD). A free-breathing 3D whole-heart sequence (MTC-BOOST) has been recently proposed for contrast-free simultaneous bright- and black-blood MRI, demonstrating high-quality depiction of arterial and venous structures. However, high-resolution fully-sampled MTC-BOOST acquisitions require long scan times of ~12min. Here we propose a joint Multi-Scale Variational Neural Network (MS-VNN) which enables the acquisition of high-quality bright- and black blood MTC-BOOST images in ~2-4 minutes, and their joint reconstruction in ~20s. The technique is compared with Compressed-Sensing reconstruction for 5x acceleration, in CHD patients.