This study investigates the impact of DNASE1L3 deficiency on hepatic immune–metabolic homeostasis using TMT-based quantitative proteomics. Liver tissues from 8-week-old wild-type (WT) and DNASE1L3 knockout (KO) mice were analyzed by LC-MS/MS. Differential protein expression and pathway enrichment analyses revealed alterations in lipid metabolism, oxidative stress, Kupffer cell polarization, and ferroptosis, supporting a role for DNASE1L3 in regulating hepatic immune–metabolic stability.