A long-term field experiment and ICP-AES analysis were conducted to study concentration and content of micronutrients Mn and Zn in maize under different fertilization systems. The results were as follows: (1) Concentrations of Mn in maize under NPKM and NPK treatments were significantly higher than those in M and control treatments. The concentration of Zn in grain of maize was similar under different treatments. The control treatment had the highest concentration of Zn in stalk, while NPKM treatment had the lowest one. (2) Contents of Mn and Zn increased with increasing yields of maize, and the regression relationship between the contents and yield of stalk was better than that between the contents and yield of grain. (3) Most of Mn and almost half of Zn were concentrated in stalk. The distribution and use efficiency of micronutrients were optimized under NPKM and NPK treatments. Returning the stalk to soil is an effective strategy for micronutrients sustainable utilization in agro-ecosystem.