1-methylcyclopropene (1-MCP) effectively delays the ripening of papaya fruit, but inappropriate 1-MCP treatments induce ripening disorders. Thus, this study aimed to clarify the roles of CpAGL18 in regulating papaya fruit ripening and the possible mechanism underlying the ripening disorder. The expression of CpAGL18, a MADS-box transcription factor, is closely related to papaya fruit ripening. Transient and ectopic overexpression of CpAGL18 promotes papaya and tomato fruit ripening. However, the transient silencing of CpAGL18 repressed fruit ripening. CpAGL18 bound and activated the promoter activities of genes in the ethylene and auxin signaling pathways, including CpERS1, CpERF224.4, CpEIN3, CpWAT1, CpIAA11 and CpIAA16-like, which were validated by the DLR, Y1H, EMSA, and ChIP-qPCR assays. CpAGL18 interacts with CpEBF1/2, and the interaction promoted the activities of CpERS1, CpERF22.4.4, CpIAA16 and CpWAT1. Additionally, it was demonstrated that CpEBF1/2 had no ubiquitination effect on CpAGL18. These data showed that CpAGL18 might act as a regulator in integrating ethylene and auxin signaling to regulate fruit ripening. The unsuitable 1-MCP severely impaired the ethylene signaling and regeneration of the new ethylene receptor of fruit by inhibiting CpAGL18 expression, possibly accounting for the ripening disorder formation.