The present invention relates to a column temperature controlling high borosilicate glass interlayer chromatography column, wherein the upper end of a chromatography column body is provided with a material inlet, a sand core is arranged inside the chromatography column body, the lower end of the chromatography column body is provided with a material outlet pipe, the material outlet pipe is provided with a material outlet control valve, the diameter of the material outlet pipe is less than the diameter of the chromatography column body, a jacket layer is arranged on the outer periphery of the chromatography column body, the outer periphery of the chromatography column body is completely surrounded by the jacket layer, a cavity is formed between the jacket layer and the chromatography column body, the jacket layer is provided with a carrier inlet and a carrier outlet, and the temperature of a heating agent is maintained at the required temperature T DEG C during the chromatography process so as to continuously supply heat for the filler in the chromatography column body and the elution solvent. According to the present invention, with the column temperature controlling high borosilicate glass interlayer chromatography column, the column separation column temperature can be well controlled, the non-room temperature separation of the temperature sensitive specific component can achieved, the separation efficiency of the soluble components in the hot solvent can be improved, and the column temperature controlling high borosilicate glass interlayer chromatography column are widely used in the column chromatography separation process requiring the column temperature control in the fields of chemistry, chemical industry and pharmacy, and has promotion values.