The structure of the Academy is determined by the tasks and directions of scientific research.  

The highest governing body is the General Assembly of the Academy members.

In the period between the sessions of the General Assembly, governing activity is accomplished by the Presidium of the Academy — the elective, permanent collegial governing body of the Academy (hereinafter referred to as the Presidium).

The Presidium organizes and manages all the activities of the Academy and is competent to resolve any issues of its activities, except for the ones related to the exclusive competence of the General Assembly.

Meetings of the Presidium are presided over by the Chairman of the Presidium of the Academy. 

The sole executive body, the highest official is the President of the Academy. In his/her absence, the interests of the organization are represented by the Deputy President.  

The Scientific Council of the Regional Public Organization “Moscow Public Academy of Natural Sciences and Humanities” is a collegiate, permanently acting advisory body of the Academy, created for the purpose of strategic development and coordination of scientific and scientific-technical activities of the Academy.

The Auditor is the control and revision body of the Academy. He / she is elected at the General Assembly by secret vote from among the members of the Academy for a specified period.

The Leaders of the scientific directions of the Academy head the creative teams of scientists formed in accordance with the main directions of scientific research approved at the General Assembly of the Academy.     

Documentation support of the meetings of the General Assembly and The Presidium of the Academy is provided by the Academic Secretary of the Presidium.