Programmed cell death is an evolutionarily conserved process essential for animal development and tissue homeostasis. Mitochondria have been demonstrated to play a central role in regulating both the activation and the execution of apoptosis. In particular, mitochondria release multiple proapoptotic factors from its intermembrane space, leading to both caspase-dependent and -independent cell death. Despite the pivotal roles of invertebrate animal models, Caenorhabiditis elegans and Drosophila melanogaster, in deciphering conserved pathways and mechanisms of programmed cell death, the importance of mitochondria to apoptosis of invertebrates remains elusive and largely unexplored. Recent studies have corroborated significant association between mitochondria and apoptosis in C. elegans, making it a thrust area of investigations. In this review, we detail the roles of mitochondrial proteins in mediating execution of cell death in C. elegans, including chromosome fragmentation, phosphatidylserine externalization, and elimination of mitochondria, and discuss the potential roles of mitochondria in the activation of C. elegans cell death. The combination of traditional powerful genetic tools and the emergence of the multiple new reverse genetic techniques, including the highly efficient CRISPR/Cas9 gene-editing method, should make C. elegans an ideal animal model for analyzing mitochondrial cell death pathways and associated regulatory mechanisms.