In order to explore the difference of selenium enrichment ability of different sweet potato strains, 22 excellent sweet potato strains independently selected by Fuzhou Institute of Agricultural Sciences were used as test materials, and ‘Guangshu 87’ with strong selenium enrichment ability was used as the control variety. 22 independently bred sweet potato strains were selected as materials, and ‘Guangshu 87’ was used as the control variety. The comparative experiment of selenium enrichment ability was carried out by spraying exogenous organic selenium fertilizer on the leaves. The results showed that: (1) Cluster analysis of selenium content in sweet potato tubers of different strains treated with selenium fertilizer showed that the strains with high enrichment and medium high enrichment types included nine strains such as ‘Rongshu 2306’, ‘Rongshu 2321’, ‘Rongshu 2310’, ‘Rongshu 2305’, ‘Rongshu 2322’ and so on. ‘Rongshu 2306’, ‘Rongshu 2301’, ‘Guangshu 87’, ‘Rongshu 2315’ and ‘Rongshu 2321’ ranked the top five in the increase rate of selenium content in tubers compared with the control. (2) There were differences in selenium accumulation of sweet potato tubers among different strains treated with selenium fertilizer. The top five strains included ‘Rongshu 2306’, ‘Guangshu 87’, ‘Rongshu 2315’, ‘Rongshu 2301’ and ‘Rongshu 2310’. The selenium absorption and utilization rates of different strains of sweet potato tubers were quite different. The strain with absorption and utilization rates of more than 5% was ‘Rongshu 2306’, and the strains with absorption and utilization rates of more than 3% included ‘Rongshu 2301’, ‘Rongshu 2315’, ‘Guangshu 87’, ‘Rongshu 2321’, ‘Rongshu 2310’ and so on. (3) Cluster analysis of selenium sensitivity of different sweet potato strains showed that ‘Rongshu 2306’, ‘Rongshu 2315’ and ‘Rongshu 2301’ were more sensitive to selenium. The selenium sensitivity index was between 0.89 and 0.91, and the yield increase rate of selenium fertilizer treatment was between 9.82% and 12.48% compared with the control. In conclusion, ‘Rongshu 2306’, ‘Rongshu 2301’ and ‘Rongshu 2315’ had strong selenium enrichment ability and high fresh tuber yield, which were suitable for planting as selenium-enriched sweet potato varieties and parent materials for breeding new selenium-enriched sweet potato varieties.