Previous research has reported that hypoxic conditions and ethylene treatments greatly trigger programmed cell death (PCD) occurrence and induce the formation of aerenchyma to adapt stress environment in Helianthus annuus stem. Caspase 3-like protease (CLP) as regulatory signals, also be involved in the process of PCD to adapt the low oxygen environment. However, the relationships between ethylene and CLP have seldom been reported. Herein, To understand the regulatory role of ethylene and CLP signaling molecules in aerenchyma formation, we investigated the effects of exogenous ethephon (ET), ethylene perception inhibitor 1-methylcyclopropene (1-MCP), and the treatment of 1-MCP + ET on morphological, physiological characteristics and aerenchyma formation in H. annuus stem. The results showed that lysigenous aerenchyma formation in H. annuus stem is induced by ET, and immunohistochemistry assay indicate CLP activity is raised at the formation stage of aerenchyma formation, and decreased at the expanding phase of aerenchyma formation. Western blotting illustrate the expression of CLP is also increased within 8h after ethylene signaling inducing aerenchyma formation, and the activities of CLP are higher in ET treated seedlings than the control and 1-MCP treated seedlings. The same phenomenon was also observed by caspase-3 activity assay. These results revealed there is a causal and interdependent relationship between ET and CLP signaling during the process of aerenchyma formation, which regulating PCD initiation in H. annuus stem.