A micro-channel distillation device was used for the process intensification method to separate boron isotopes, 10B and 11B. Three-dimensional (3D) printing technology was introduced to manufacture the micro-channel device, which used the chemical exchange method with anisole as the donor to separate the boron isotopes. This device was tested in total reflux mode, and the height of an equivalent theoretical plate of the micro-channel distillation equipment was reduced to 1.56 cm. The accurate control of pressure and temperature, as well as the flow rate of the complex, were factors that affected separation ability. Thus, for process intensification, this micro-channel distillation device can be operated horizontally and connected in series into similar modules to effectively improve separation efficiency and reduce the size of the equipment.