Flowers are reproductive plant organs that determine final fruit or seed yield. SEPALLATA-like MADS-box genes participate in floral determination and/or flower organ specification. Nevertheless, their molecular mechanisms in bell pepper have not yet been elucidated. In this study, we identified CaSEP5, which encodes a duplicated SEPALLATA-like MADS-box protein grouped in the FBP9/23-subclade. CaSEP5 genes were detected in all whorls of floral organs, and were relatively highly expressed in the sepals and petals. Subcellular localization revealed that CaSEP5 was in the nucleus. This finding aligns with transcription factor characteristics. The physical interactions of CaSEP5 with B-, C-, and other CaSEPs indicated that CaSEP5 act as glue to form protein complexes to regulate flower development by altering the hormones level and distribution. CaSEP5-silenced plants had elongated, leaf-like sepals, rigid, straight pedicels, reduced fruit size, altered expression patterns of other floral homeotic genes, and varied hormone levels. We proposed that CaSEP5 plays an important role in pepper flower and fruit development by means of a complex hormone and genetic network.