Miniaturized machines have open up a new dimension of chemistry, studied usually as an average over numerous molecules or for a single molecule bound on a robust substrate. Mechanical motions at a single molecule level, however, are under quantum control, strongly coupled with fluctuations of its environment — a system rarely addressed because an efficient way of observing the nanomechanical motions in real time is lacking. Here, we report sub-millisecond sub-Å precision in situ video imaging of a single fullerene molecule shuttling, rotating, and interacting with a vibrating carbon nanotube at 0.625 milliseconds(ms)/frame or 1600 fps, using an electron microscope, a fast camera, and a denoising algorithm. We have achieved in situ observation of the mechanical motions of a molecule coupled with vibration of a carbon nanotube with standard error as small as 0.9 millisecond in time and 0.01 nm in space. We have revealed rich molecular dynamics, where motions are non-linear, stochastic and often non-repeatable, and a work and energy relationship at a molecular level previously undetected by time-averaged measurements or microscopy. The molecular video recording at a 1600-fps rate exceeds by 100 times the previous records of continuous recording of molecular motions.