The dynamics of effectiveness and structural characteristics of the system of motivation of scientific activity within some years after the defense of a doctoral thesis is analyzed. The sample included 57 Doctors of Sciences who defended their theses from 1 to 7 years ago. The results show that the level motivation of scientific activity and its functional capacities goes down abruptly after the defense of a doctoral thesis. It has a destabilizing effect on the psychological system of a scientific activity on the whole and has an impact of its efficiency. Functional capacities of the motivation system of a scientific activity of Doctors of Science restore within 4–7 years after the thesis defense. To optimize restoration of functional capacities of motivation system of a scientific activity, psychological follow-up aimed at restoring motivation resources is recommended.