Cytoplasmic invertase (CIN) irreversibly hydrolyzes sucrose into glucose and fructose and plays an important role in the development of roots in various model plants. Presently, there is no research on the CIN gene family in sweetpotato (Ipomoea batatas) and the role of IbCINs in the development of storage roots of sweetpotato remains to be elucidated. This study systematically identified the types and quantities of IbCIN gene family. Physicochemical properties, chromosome localization, phylogeny, gene structure and conserved motifs, promoter cis elements of IbCINs were also analyzed. Simultaneously, through the expression analysis of IbCINs in different tissues and different types of roots, and the activity analysis of CIN in different types of roots, several candidate CIN genes were identified that play an important role in the development of storage roots of sweetpotato. A total of 12 IbCIN genes (IbCIN1-12) were identified from the genome of sweetpotato, distributing on 8 chromosomes. The number of amino acids of IbCIN-encoded protein was 417-825 aa, the molecular weightwas 46.60-93.75 kDa, and the isoelectric point was 4.83-7.17. Phylogenetic analysis revealed that IbCINs could be divided into three groups, α1, α2 and β groups, comprising 1, 3 and 8 members, respectively. α1 and α2 members were very conservative in conserved motifs and gene structures, while β memberswere less conservative, which indicating that β group may have more diverse function than the other two groups, allowing β members to participate in more biological processes. In addition, phylogenetic analysis also revealed that IbCIN1, IbCIN7, IbCIN10 and IbCIN12 were closely related to CIN genes related to root development in Arabidopsis and cassava, suggesting that the four genes may play important roles in the development of non-storage root of sweetpotato. The analysis of the expression levels of IbCINs in different tissue (young leaves, mature leaves, stems, flowers, 60 d storage roots) and different types of roots (white fiber roots, red fiber roots, pencil roots and 60 d storage roots) showed that IbCIN4, IbCIN8 and IbCIN11 had the highest expression levels in storage roots, and simultaneously the CIN activity in storage roots was significantly higher than that in non-storage roots. Thus, it can be speculated that the three genes may play an important role in the development of storage roots of sweetpotato. Bioinformatics analysis further revealed that IbCIN4, IbCIN8 and IbCIN11 may jointly promote the development of storage roots via different mechanisms, including facilitating sucrose transport to and subsequent degradation in storage roots, attenuating photoperiod response and signal transduction of gibberellin. This study could lay a foundation for further research on the function of IbCIN genes through transgenic technology.