We performed a field plot experiment (2015-2016) to study the effects of different fertilization modes on phosphorus (P) losses by surface runoff, the apparent P balance, and vegetable and rice yield in a vegetable-rice rotation field in Taihu Lake Basin, China under natural rainfall conditions. The results showed that surface runoff events were mainly distributed in the rice growing season with heavy rainfall (rainy and typhoon season), which showed a significant positive linear correlation between the quantity of surface runoff water and rainfall capacity. And, phosphorus (TP) loss by surface runoff was also mainly distributed in the rice growing season, which accounted for 74.75%~81.46% of TP loss during the whole monitoring period including the vegetable and rice growing seasons. In T1 (conventional fertilizer application), the average TP concentration of surface runoff water in the vegetable growing season (0.55 mg/L) was significantly higher than that of rice growing season (0.29 mg/L), but TP loss (0.49 kg/hm²) was significantly lower than that of rice growing season (2.13 kg/hm²). Compared with T1, T2 (reducing application 31.17% of P compared with T1) and T3 (reducing application 49.75% of P compared with T1, in which, no P application during the rice growing season, and wheat straw biochar application during the vegetable growing season) could significantly reduce TP losses by surface runoff by 22.48% and 45.66% during the whole monitoring period, respectively. Furthermore, P surplus reached up to 260.90 kg/hm², which showed significant fertilization mode dependence and growing season dependence. In which, P surplus mainly occurred in the vegetable growing season, which accounted for 70.63% of that in the whole monitoring period. Compared with T1, P surplus in T2 and T3 decreased significantly by 38.47% and 64.87%, respectively. Moreover, compared with T1, vegetable yield decreased significantly under T2 and/or T3, but no significant difference was found between T2 and T3 in vegetable yield, rice grain yield, and annual yield of vegetable and rice grain. These results suggested that no P application during rice growing season and appropriate wheat straw biochar application during the vegetable growing season had synergistic effect of phosphorus reduction, maintaining stable crop yield and apparent P balance in the vegetable-rice rotation field.