Soluble iron and sulfate in acid mine drainage (AMD) can be greatly removed through the formation of minerals facilitated by seed crystals. However, the difference in the effects of jarosite and schwertmannite as endogenous seed crystals to induce AMD mineralization remains unclear. This paper intends to study the effect of Fe2+ oxidation and Fe3+ mineralization in the biosynthesis of minerals using different addition amounts and methods of jarosite or schwertmannite. The results showed that the addition amount and method of different seed crystals had no effect on the Fe2+ bio-oxidation but would change the Fe3+ mineralization efficiency. With the same amount of seed crystals added, jarosite exhibited a higher capacity to promote Fe3+ mineralization than schwertmannite. Adding seed crystals before the initiation of Fe2+ oxidation (0 h) could significantly promote Fe3+ mineralization efficiency. With the increase of seed crystals, jarosite could not only shorten the time required for mineral synthesis but also improve the final mineral yield, whereas schwertmannite could only shorten the time required for mineral synthesis. When Fe2+ was completely oxidized to Fe3+ (48 h), the supplementary of jarosite could still effectively improve Fe3+ mineralization efficiency, but the addition of schwertmannite no longer affected the final mineralization degree.