The invention discloses a self-alignment bipolar transistor which defines an emitter region window and a self-alignment injection region of an outer base region through a medium layer of an emitter region window and can achieve good alignment between an emitter region and the outer base region. The emitter region is formed by polycrystalline silicon which is formed in the emitter region window, coupling regions of the emitter region and the outer base region can be reduced, therefore stray capacitance between the emitter region and the base region can be lowered, and finally a frequency characteristic and performance of a device can be improved. The invention further discloses a preparation method of the self-alignment bipolar transistor. According to the preparation method, injection of the outer base region is self-alignment injection, and therefore a photo-etching layer forming the outer base region can be eliminated, and process cost is lowered. Moreover, when the emitter region is formed, back-engraving carried out on the emitting electrode polycrystalline silicon is overall back-engraving, and therefore a layer of a photo-etching mask plate can also be eliminated, and process cost and complexity can be lowered.