To further investigate the response of biogeochemical cycle of Ca and Mg to atmospheric CO2 enrichment, a study associated with the medium-long term effects of elevated CO2 on transposition of Ca and Mg at three soil depths (30, 60, and 90 cm) in different developmental stages was carried out on China rice-wheat rotation FACE (Free Air Carbon-dioxide Enrichment) experimental platform in the rice growing season. The results showed that with the increment in the soil depth, the Ca2+ concentration in soil solution showed a trend of decrease, and the Mg2+ concentration was increasing; whereas they increased at first and decreased then, and peaked at heading stage. Atmospheric CO2 enrichment slightly decreased the Ca2+ concentration in the soil solution at 30 and 60 cm, but enhanced it at 90 cm (6.7%). It was detected that the responses of Mg2+ concentration in the soil solution to elevated CO2 differed with the soil depth, and a stronger positive response was found at 60 cm (12.1%). This study indicated that elevated CO2 tends to intensify the leaching loss of Ca2+ and Mg2+, the increase in organic materials input andconcentration, and decrease in pH in the plow layer are the main causes. The long term effects of elevated CO2 on Ca and Mg cycle in the soil under agricultural ecosystems deserve a further attention to pay.