The invention relates to a multifunctional mixed structure type counter-current chromatograph which comprises a base, a supporting device, a drive device, a rotation device and multiple separation units; the multiple separation units include arbitrary combination of an orthogonal separation unit, a parallel separation unit and an inclined separation unit. The multifunctional mixed structure type counter-current chromatograph is a new structure which is evolved from structure combination of the existing parallel axis counter-current chromatograph, orthogonal axis counter-current chromatograph and inclined axis high-speed counter-current chromatograph. For the multifunctional mixed structure type counter-current chromatograph, one revolution and one rotation of an orthogonal axis separationcolumn are realized by adopting a planetary bevel gear, one revolution and one rotation of an inclined axis separation column are realized by adopting planetary bevel gears with different included angles, one revolution and one rotation of a parallel axis separation column are realized by adopting planetary bevel gears, and movements of the three kinds of the separation columns are mutually independent without mutual influence; and the multifunctional mixed structure type counter-current chromatograph has the advantages of strong adaptability, high separation efficiency, comprehensive functions and the like and can be applied to separation and purification of natural bioactive macromolecules such as substances of proteins and active peptides.