The soil nutrient limiting factors of seed lotus yield was verified in Guangchang county，Jiangxi province，in order to provide scientific basis for guiding the rational application of fertilizers in seed lotus production. Micro-plot experiments (2.25 m2) were conducted to study the effects of combined application of nitrogen，phosphorus，potassium，magnesium and boron fertilizers on the yield and its components of seed lotus in the lotus field with low magnesium and boron. The results showed that the combined application of nitrogen，phosphorus，potassium，magnesium and boron(BF) significantly increased the yield of seed lotus. Compared with the BF treatment，the yield of seed lotus decreased by 52.4%，9.5%， 21.9%，36.2% and 15.7%，respectively，in the treatments of no nitrogen，phosphorus，potassium，magnesium and boron fertilizer applied on the basis of BF treatment. The effects of different fertilizers on the yield of seed lotus in low magnesium and boron soil was ranked in nitrogen>magnesium>potassium >boron >phosphorus. The results of yield dynamics showed that the lack of nitrogen，phosphorus，potassium，magnesium and boron fertilizers shortened the rapid increase period of seed lotus，and the yield increment in the middle and late stages of harvest decreased. It was necessary to extend the rapid growth period and increase the growth rate during the growth period to obtain the higher yield. The results of yield components of seed lotus showed that the deficiency of any nutrient of nitrogen，phosphorus，potassium，magnesium and boron would affect the effective receptacle numbers，the average carpels number per ten days，the average seed setting rate per ten days，and the average single seed weight per ten days. Specifically，nitrogen fertilization significantly increased the effective receptacle numbers，the average carpel numbers per ten days and the average single seed weight per ten days. Boron fertilization increased the effective receptacle numbers and the average single seed weight per ten days. Meanwhile phosphorus，potassium and magnesium fertilization increased the effective receptacle numbers. In conclusion，the combined application of nitrogen， phosphorus，potassium，magnesium and boron could significantly enhance the yield of seed lotus on the low magnesium and boron soils. The yield of seed lotus increased by improving the effective receptacle numbers，the average carpels numbers per ten days，the average seed setting rate per ten days，and the average single seed weight per ten days of seed lotus. During the seed lotus growing，the yield can be increased by prolonging the rapid increase period and increasing the growth rate.