Synchrotron radiation X-ray fluorescence analysis technology (SRXRF) can effectively reduce the detection limit for the determination of heavy metal elements. The technique is especially suitable for in situ nondestructive analysis of biological samples with low contents. By corn seed germination test, and combining with SRXRF technique, the effects of Pb on corn seed germination and Pb micro-distribution in the corn seed were studied. X-ray absorption near edge structure (XANES) technique was also used to analyze the Pb chemical speciation in different parts of corn seed. The above experiments were carried out for understanding the absorption and transformation mechanism of Pb by corn seeds. The results showed that the germination rate, bud length and root length decreased with the increasing contents of Pb. The analysis of variance showed that P-value of the germination rate, bud length and root elongation of corn seeds which were exposed to different concentration of Pb were 2.0 × 10−3, 1.4 × 10−4 and 2.4 × 10−8 respectively, suggesting there were highly significant differences during this three indicators and the content of Pb. In addition, the inhibition effect on root growth was greater. The results of SRXRF analysis showed that Pb was mainly enriched in episperm and embryo, which would inhibit embryonic develop into bud and root. Moreover, the results showed that all samples including root, shoot and the different part of seed had the same Pb-LIII (13035 eV) XANES spectra and Pb speciation. The linear combination fitting results indicated that the lead phosphate chloride and lead stearate accounted for 74.3% and 24.2% respectively, suggesting that the main Pb speciation in corn was lead phosphate chloride which deposited inside of corn, and a few combined with carboxylic to form organic lead.