Purpose: To develop and validate a highly efficient motion compensated free-breathing isotropic resolution 3D whole-heart joint T-1/T-2 mapping sequence with anatomical water/fat imaging at 0.55 T. Methods: The proposed sequence takes advantage of shorter T-1 at 0.55 T to acquire three interleaved water/fat volumes with inversion-recovery preparation, no preparation, and T-2 preparation, respectively. Image navigators were used to facilitate nonrigid motion-compensated image reconstruction. T-1 and T-2 maps were jointly calculated by a dictionary matching method. Validations were performed with simulation, phantom, and in vivo experiments on 10 healthy volunteers and 1 patient. The performance of the proposed sequence was compared with conventional 2D mapping sequences including modified Look-Locker inversion recovery and T-2-prepared balanced steady-SSFP sequence. Results: The proposed sequence has a good T-1 and T-2 encoding sensitivity in simulation, and excellent agreement with spin-echo reference T-1 and T-2 values was observed in a standardized T-1/T-2 phantom (R-2 = 0.99). In vivo experiments provided good-quality co-registered 3D whole-heart T-1 and T-2 maps with 2-mm isotropic resolution in a short scan time of about 7 min. For healthy volunteers, left-ventricle T-1 mean and SD measured by the proposed sequence were both comparable with those of modified Look-Locker inversion recovery (640 +/- 35 vs. 630 +/- 25 ms [p = 0.44] and 49.9 +/- 9.3 vs. 54.4 +/- 20.5 ms [p = 0.42]), whereas left-ventricle T-2 mean and SD measured by the proposed sequence were both slightly lower than those of T-2-prepared balanced SSFP (53.8 +/- 5.5 vs. 58.6 +/- 3.3 ms [p < 0.01] and 5.2 +/- 0.9 vs. 6.1 +/- 0.8 ms [p = 0.03]). Myocardial T-1 and T-2 in the patient measured by the proposed sequence were in good agreement with conventional 2D sequences and late gadolinium enhancement. Conclusion: The proposed sequence simultaneously acquires 3D whole-heart T-1 and T-2 mapping with anatomical water/fat imaging at 0.55 T in a fast and efficient 7-min scan. Further investigation in patients with cardiovascular disease is now warranted.