The accumulation of phosphorus (P) in soil profiles of intensive cropland and the losses caused by runoff and leaching have been widely concerned. However, the loss of soil P due to shallow groundwater table (SGT) fluctuations driven by seasonal changes is often neglected, and the migration and transformation mechanisms of soil P are still unclear. On the basis of the long-term monitoring of cropland soil P accumulation and SGT fluctuations around Erhai Lake, the characteristics of soil P loss driven by SGT fluctuations and the corresponding mechanisms were investigated through a 260-day microcosm experiment. The results revealed that the fluctuations in SGT significantly changed the content and form of P in the soil profile. The soil P loss mainly occurred in dissolved form, mainly involving inorganic P, accounting for 75 %. Compared with those under continuous saturated conditions, soil total P (TP) release during SGT fluctuations significantly increased by 9.5 %, and soil TP storage was reduced by 2 %. SGT fluctuations increased the complexity of microbial networks in the soil profile, stimulated the expression of functional genes for soil P cycling, and promoted soil organic P mineralization. The SGT fluctuations caused an increase in the soil TP loss from cropland to 88.5 kg/ha, which was 70 and 25 times greater than that via leaching and runoff, respectively. These results indicated that SGT fluctuations accelerated the P loss from soil profile of cropland. Therefore, some measures should be comprehensively applied to prevent its loss, such as reducing external P input, improving surface soil P storage capacity and soil P utilization efficiency, reducing surface P leaching into deep soil, and reducing P accumulation in deep soil profiles.