According to its bylaws, the Saxon Academy is an association of scholars with the purpose of serving the public good by furthering the sciences, extending and deepening scientific knowledge through research, stimulating and fostering scientific investigations and projects. It is structured in three equal Classes: the Mathematical-Natural Sciences Class, the Philological-Historical Class and the Class of Engineering Sciences. The first two Classes have existed since the founding of the Academy, and the third began its work in 1996.

Each Class consists of up to 30 full members who have their place of residence or employment in the states of Saxony, Saxony-Anhalt or Thuringia, and of up to 30 corresponding members. The full members in their totality constitute the Plenum of the Academy. They meet as a rule once a month to take decisions on basic scientific-scholarly matters, but above all to present in lecture form their research findings and to discuss these in an interdisciplinary dialogue. At present, there are also two honorary members of the Society of Scholars.

The Academy is directed by the Presidium or Board of Regents. It consists of the President, the Vice-President, the Secretaries of the three Classes and their deputies, and the Secretary-General. In accord with the research work of the Academy, the Plenum creates structural and project-oriented commissions. Structural commissions are working commissions. In the framework of specialist conferences and symposia, they regularly organize discussions on questions of future development in individual areas of science. Project-oriented commissions bear scientific responsibility jointly with the project director for the respective projects associated with the Academy.