The structural dynamics of the clamshell rotation of photodissociated carbonmonoxy myoglobin, which is expected to be important for hemoglobin allostery, is investigated by the perturbation ensemble method. In this method, many pairs of perturbed and unperturbed molecular dynamics trajectories are ensemble-averaged to cancel out thermal noises and to detect subtle changes. The number of MD trajectory pairs, in this work 2000 pairs, should be determined to obtain physical properties of interest with statistically meaningful precisions. The calculated structural changes after 20 Ps of the photodissociation are consistent with those by time-resolved X-ray diffraction at 100 Ps delay time. In the heme proximal side region including the F and H helices, both helices displaced in the proximal direction. Meanwhile, in the heme distal side region including E and A helices, both helices moved toward the heme group after photodissociation. These proximal and distal side displacements occur on a fast time scale (almost complete within 3 ps) and are consistent with the clamshell rotation. Moreover, it was found that the ensemble-averaged structural dynamics of the photodissociated MbC0 is independent of the amount of initial excess vibrational energy of the heme, or the difference of excitation photon wavelength. These results provide atomistic details on the functionally important dynamics of the clamshell rotation. Application of the present methodology to lib will give new insight into the incipient stereochemical mechanism of hemoglobin allostery.