Abstract: A set of dosimetry system with graphite ionization chamber for low energy proton beams was set up. The characteristics of self-developed graphite ionization chamber were studied. The results show that the self-developed graphite ionization chamber meets the requirement of standard ionization chamber. Transmission ionization chamber was designed and used to monitor the change of proton beams online, which increased the accuracy of results when calibrating the other dosimetry systems. Absorbed dose of low energy proton was measured by using self-developed dosimetry system with ionization chamber, and the composed standard uncertainty is 4%. The calibration method of alanine dosimeter was researched in the HI-13 Tandem Accelerator, and the RE specific values were obtained for the different proton energy.