The Structural Maintenance of Chromosomes complex 5/6 (SMC-5/6) safeguards genome stability by coordinating DNA replication, repair, and chromosome organization. Although prior studies have advanced understanding of SMC-6, a domain-resolved view of its functions in vivo, particularly in multicellular organisms, remains incomplete. Because the non-SMC subunit NSE-1 localizes at the SMC-5/6 head interface and reflects complex integrity, we used NSE-1::GFP nuclear localization as a visual readout in an ethyl methanesulfonate (EMS)-based forward genetic screen in Caenorhabditis elegans (C. elegans). We identified three new smc-6 alleles—smc-6(wsh34), smc-6(wsh35), and smc-6(wsh36) through single-nucleotide polymorphism (SNP) mapping and whole-genome sequencing. smc-6(wsh34) and smc-6(wsh35) affect the N-terminal ATPase domain, whereas smc-6(wsh36) lies in the hinge region. ATPase-domain mutants exhibited reduced fertility, decreased progeny viability, hypersensitivity to methyl methanesulfonate and cisplatin, and strong induction of the pro-apoptotic genes egl-1 and ced-13. In contrast, the hinge mutant exhibited moderate fertility defects and partial sensitivity to DNA damage reagents. Structural modeling suggests that the R103 truncation disrupts the SMC-5/6 head interface, whereas the P514L substitution alters hinge dynamics. Together, these findings reveal a functional hierarchy in SMC-6, with the ATPase domain governing repair-associated energy-dependent processes and the hinge maintaining structural integrity.