The concentration and distribution of Mn and Zn in soil and soybean in lower reach of Liaohe River Plain were investigated with ICP-AES analysis. The results showed that the available Zn in soils was close to the critical value and the monitoring should be strengthened. Zn concentration in seed and stalk, coupled with Mn in stalk, was not affected by fertilization types, while Mn concentration in seed under NPK and NPKO treatments was significantly higher than that with O and CK treatments. Application of organic and inorganic fertilizer increased crop biomass, and consequently increased Mn and Zn storage in soybean. In soil-crop system, Mn and Zn under different fertilization regimes showed budget deficit, with the deficit order of NPKO＜O＜CK＜NPK, indicating that nutrient cycling could decrease the deficit significantly and keep the ecological systems more sustainable.