The low molecular organic sodium commonly existed in the environment can affect the biomineralized products (schwertmannite and jarosite) of Acidithiobacillus ferrooxidans (A. ferrooxidans), which can lead to changes in the migration and transformation of toxic heavy metals in the environment. This paper discussed the influence of low molecular organic sodium salts on the bacterially metabolized iron minerals during the growth process of A. ferrooxidans HX3, and also characterized and analyzed the iron minerals by XRD, FTIR, FESEM and EDS. The study results showed that the addition of low molecular organic sodium salts at the lower concentrations had unobvious effects on the Fe²⁺ oxidation, but it could accelerate the formation of jarosite. Addition of sodium malate was conducive to the transformation of schwertmannite to jarosite, compared with addition of sodium citrate or sodium oxalate. Addition of the low molecular organic sodium salts at the higher concentration (i.e. 20, 40 and 40 mmol/L for sodium malate, sodium citrate and sodium oxalate, respectively) inhibited the oxidation of Fe²⁺ during bacterial cultivation process. The sequence of inhibitory effects from large to small was following: sodium malate>sodium citrate>sodium oxalate. These results could provide a theoretical reference for the formation and transformation of iron minerals in acid mine wastewater containing iron bacteria such as A. ferrooxidans, and their biomineralization mechanism.