The invention discloses a direct injection type ion beam accelerator, which comprises an ion source, a beam current pipeline and an accelerating cavity, wherein the ion source is used for generating iron beams, the beam current pipeline is used for connecting the iron source and an accelerating cavity, the accelerating cavity is used for accelerating, focusing and transmitting the low energy ion beams as well as alternating phase focusing, and the accelerating cavity is an accelerating cavity realizing alternating phase focusing through adjusting position and length of a drift tube inside the accelerating cavity. Through the structure, the direct injection type ion beam accelerator can accelerate the low energy ion beams simply and conveniently, increase accelerating gradient and reduce high-frequency power consumption.