Provided are a device and method for rotatably machining a microstructure in a glass capillary. The device comprises a femtosecond laser, the device is characterized by further comprising a fixing device which is arranged on a micromachining work table and locates the glass capillary, a rotating device which drives the glass capillary to rotate so as to conduct rotary machining and a cleaning device used for sucking photoresist into the glass capillary and removing the photoresist. According to the device, the making process is simple and easy to operate, the cost is low, the use method is simple and clear, the glass capillary can achieve a rotary photoetching effect accurately, conveniently and rapidly, absolute ethyl alcohol can be rapidly and effectively charged into the glass capillary, residual photoresist obtained from photoetching in the glass capillary is cleaned, ultra violet irradiation is conducted, and therefore the microstructure in the glass capillary is effectively shaped.