Clostridium perfringens is a major pathogen threatening livestock health. This study investigated the antimicrobial resistance and genomic features of C. perfringens isolates from sheep in northern China. From October 2023 to June 2024, 70 strains were isolated from 467 fecal samples collected in Jilin, Heilongjiang, Liaoning, and Shandong provinces, with an overall isolation rate of 15.0%. The rate was significantly higher in diarrheic samples (18.07%) than in non-diarrheic ones (11.5%). Toxin gene typing identified 67.1% of isolates as type A and 32.9% as type D. Antimicrobial susceptibility testing showed that 94.3% of isolates were resistant to at least one antibiotic, with the highest resistance to gentamicin (GEN, 78.6%). Whole-genome sequencing identified seven classes of antimicrobial resistance, comprising 59 resistance genes. Additionally, 121 virulence-associated genes belonging to eight virulence factor categories were detected. Spearman correlation analysis revealed strong negative correlations between ARGs and VFGs in C. perfringens, including ErmQ vs. nagI (r_s = -1) and tetB(P) vs. cpe (r_s = -1), all remaining significant after multiple testing correction. These results suggest an adaptive trade-off in which resistance may be prioritized over virulence, highlighting a potential intrinsic antagonism between resistance and pathogenicity. Overall, C. perfringens isolates from sheep exhibit high resistance and genetic diversity, highlighting the importance of surveillance and prudent antimicrobial use to reduce potential public health risks.