The water saturated Arabidopsis seeds were irradiated with protons in air. The ion energy is from 1.1MeV to 6.5MeV. According to TRIM simulation, the damaged region of the seed induced by the incident ions is near the surface region of the embryo, half of the embryo and the whole embryo, respectively. The protons with high energy can damage the shoot apical meristem(SAM) in the embryo while the protons with low energy cannot. The ion fluence used in this experiment was in the range of 4×109 to 1×1014ions/cm2. The experimental results showed that both the germination and survival rates decrease while increasing ion fluence, and the fluence-response curve for different damaged region of the embryo has different characters. Besides SAM, which is generally considered as the main radiobiological target, the existence of a secondary target besides SAM is proposed in this paper.