In order to assess the cardiovascular physiology of bivalves living in deep-sea hydrothermal vents and seeps, the Calyptogena okutanii was collected at depths of around 860 m at the Off Hatsushima seep site. The anatomical structure and function of the heart of the clams were studied by T1-weighted magnetic resonance imaging (T1w-MRI) at atmospheric pressure in seawater without sulfide supply at 10 °C. In the 58 MRI sessions employing 5 clams at 2–3 days after sampling, the average heart rate was 6.5 ± 2.0 beats·min−1, which was lower than the average of 5 individual Bathymodiolus platifrons (10.3 beats·min−1). A regular rhythm was observed in 50% of the sessions, and arrhythmia (including cardiac arrest) appeared in the remaining sessions. The arrhythmia appeared more frequently than the regular heartbeat during sessions with foot motion. Indeed, a short cardiac arrest was often observed during extension of the foot, and the heartbeats restarted when the foot was withdrawn into the shell. The ejection fraction of the ventricle of C. okutanii (75%) was higher than those shown by the Mytilus and human. In a separate experiment, the heart rate of 2 clams was measured for 7 days after sampling. Foot motion was hardly observed after the 6th day, and the faster and slower components of the heart rates decreased and increased from the 5th day after sampling, respectively. Judging from these results, the pattern of the heart rate frequency distribution might be useful to assess the vital condition of C. okutanii.