This work is devoted to the description of the orbital and magnetic structures of pure and charge-ordered manganites, caused by crystal and charge structures and the Jahn–Teller effect. The model under consideration is based on the orbital dependency of the magnetic interactions in Jahn–Teller crystal. The orbital structure is considered dependent upon the Jahn–Teller distortions of the coordination of the Mn3+ ions and upon the crystal field. It is shown that exchange interactions forming the magnetic structure of the charge-ordered manganite could be described in the superexchange approximation because of localization of the charge carriers. For pure manganite and for charge-ordered phase, the exchange parameters dependencies and the single-ion anisotropy dependency, upon the angle of orbital states mixing, are drawn. Therefore, it is shown that the orbital structure of the charge-ordered phase is formed mainly by cooperative Jahn–Teller distortions and, taking into account the charge superstructure, causes the non-trivial magnetic structure.