The available soil microelements are important components of enzyme, growth hormone and vitamins in plants. A better understanding of the variability of soil microelements after Grain for Green project will improve the emphasis of afforesting during the proceeding period. However, quantitative research on the effect of Grain for Green project on soil microelements is quite scarcity. The study was conducted to ascertain the effect of Grain for Green project on soil microelements (Cu, Zn, Mn, Mo and Fe) in Guanchuan river basin of Loess Plateau by applying partial correlation analysis and path analysis. The results showed that the contents of available soil microelements were promoted as a whole but diminished with the increase of soil depth after croplands were converted into forest lands. Available Fe in the soil was at a below level and could not meet the demands of plant growth. The available indices of soil microelements in forest lands were higher than those in croplands, the available amounts of Cu, Mn and Mo were higher than those of Zn and Fe. Moreover, Platycladus orientalis forest lands showed a higher comprehensive index than Picea asperata forest lands. Partial correlation analysis and path analysis showed that principal influence factors of variation in soil microelements were soil organic matter, soil total K, soil total N and soil moisture content. Both soil K and organic matter had a significant positive correlation with available Cu, Zn and Fe. Regression analysis showed that soil environmental factors can explain 38.1%~73.8% of variation in soil microelements. Decision-making analysis showed that soil K and soil organic matter were decision variables in soil microelements, while the soil moisture content was the limited variable in the experimental region. It was recommended that application of rainwater harvesting measurements can improve utilization efficiency of precipitation. The results provide valuable reference for implementing the Grain for Green project in semi-arid region.