Abstract: In order to improve the food safety of infant soybean-based formula powder, the soybean protein preparation processes which include pulping, extraction, acid-precipitation and water-washing were innovated. The effects of wetting, blanching and semi-dry pulping processes and key steps on protein extraction rate, phytic acid and isoflavone removal rate were studied. Results showed that when protein extraction solution was made by semi-dry method, and protein was extracted by precipitation at pH5.15, followed by washing and centrifugation, the levels of phytate and isoflavones could be well limited, where the retention of whey fraction should be lower than 20%. The concentrations of phytate and isoflavones were respectively (12.08±0.46) mg/g and (1468±74) μg/g. The higher removal rate of phytate and isoflavones facilitated improved the safety of the protein product, which laid a foundation for further development of soy protein-based food ingredient tailor-made for infant formula, with improved safety and quality.