Abstract: To found the influence rule of trace elements on seed yield and seed characteristics and provide reference for rational use of trace elements in alfalfa seed production, Medicago sativa L.‘Xinmu No.4’was used as the material and trace elements boron, molybdenum, iron at different concentrations were sprayed during the budding stage of alfalfa. Effects of different trace elements on blossom and fruiting characteristics of alfalfa were studied by measuring the floral traits, podding rate, seed yield, seed characteristics and so on. The results showed that seed number per pod and seed yield of alfalfa were 9.67% and 35%, 12.9% and 17%, 7.5% and 69.46% higher than that of the control group when spraying 4 kg/hm2 borax, 325 g/hm2 ammonium molybdate, 3 kg/hm2 ferrous sulfate, respectively. But podding rate of each treatment group was lower than that of the control group (59.66%). Correlation analysis showed that seed yield of alfalfa had significantly positive correlation with podding rate, seed number per pod and thousand seed weight. Comprehensive analysis revealed that spraying borax, ammonium molybdate and ferrous sulfate at the concentration of 2.98 kg/hm2, 325 g/hm2 and 2.90 kg/hm2 respectively could increase seed number per pod, thousand seed weight and improved seed yield of alfalfa in Changji area of Xingjiang.