To understand of hydrolysis characters of Arabidopsis thaliana phytase(ATMINPP), we applied bioinformatics, homology modeling and molecular docking methods to predict and analysis the structure of ATMINPP and its interaction with the phytic acid. The results showed that ATMINPP consists of 487 amino acids, and its secondary structure consists of 18 alpha helices, 6 beta sheets, stretch fragments and random coils. Conserved cysteine forms four disulfide bonds between helices. The protein has two structural domains, namely α/β-domain and α-domain, and the active site localizes at the junction of two structural domains. Docking with the phytic acid, the negatively charged inositol hexaphosphate binds to the positively charged hydrophilic pocket of the ATMINPP. Meanwhile, the negatively charged phytic acid combines with a positively charged hydrophilic pocket within ATMINPP. His 66 in the conservative sequence of RHGARYP conducts a nucleophilic attack on the phosphorus atom bound by the phytic hydrogen bond to form an intermediate complex. It is hydrolyzed to give phosphoric acid and phosphositol derivatives. His 343 of ATMINPP provides protons to dissociate the group oxygen atom, causing the phosphate group to dissociate.