Abstract: 【Objective】 To develop a seed coating agent which can effectively control two kinds of root rot diseases of cotton at seedling stage: Rhizoctonia solani K. and Fusarium verticillioides spp. 【Method】 The raw drugs of carboxin and fludioxonil were selected as the main components, the growth rate method was used to determine the bacteriostatic effects of different seed coating formulations on two kinds of pathogenic bacteria, indoor germination and pot experiments were used to verify its safety and growth-promoting effect on cotton seedlings, and the comparison of disease control and yield increase was carried out indoors and in the field. 【Result】 The principal component analysis showed that the bacteriostatic effect and cotton seedling growth-promoting effect of the seed coating agent with the compound ratio of 7.2 carboxin and 1.0 fludioxonil was the best, and it was better than the commercial seed coating agent 20% tolclofos-methyl ·thiram. Through indoor pot inoculation experiments and field verification, it was found that the compound ratio of 7.2∶1.0 had the best effect on disease control and yield increase. Its control effects on opposite blight and red rot were 87.19% and 88.30%, respectively. In the field, the control effects on the two diseases were 75.79% and 66.3%, respectively, and the yield-increasing effect reached 9.11%. 【Conclusion】 The best formulation of seed coating agent of carboxin and fludioxonil was 7.2∶1.0. This kind of coating agent was effective to control root rot diseases of cotton at seedling stage, which had a certain yield-increasing effect.