Purpose To eliminate the effects of field strength in determining the diagnostic performance of the LI-RADS version 2018 (LI-RADS v2018) in differentiating hepatocellular carcinoma (HCC) from non-HCC primary liver malignancy in high-risk patients. Methods Patients who were pathologically confirmed intrahepatic cholangiocarcinoma (iCCA) or combined hepatocellular-cholangiocarcinoma (cHCC-CCA) were retrospectively reviewed. Patients with HCC were matched to the iCCA or cHCC-CCA patients on age, tumor size, MR scanner, and number of tumors. Two readers independently evaluated the lesions according to LI-RADS v2018. Diagnostic performance of LI-RADS v2018 in differentiating HCC from non-HCC primary liver malignancy were analyzed. Results A total of 198 patients with 204 lesions (102 HCCs, 78 iCCAs, and 24 cHCC-CCAs) were enrolled. The sensitivity and specificity of LR-5 or LR-TIV (definitely due to HCC) in diagnosing HCC were 68.63% and 85.29%, respectively. LR-M or LR-TIV (may be due to non-HCC malignancy) had a sensitivity of 72.55% and a specificity of 86.27% in diagnosing non-HCC malignancy. The sensitivity of LR-M or LR-TIV (may be due to non-HCC malignancy) for iCCA and cHCC-CCA was 82.05% and 41.67%, respectively. Nearly half (11/24, 45.83%) of cHCC-CCAs were categorized as LR-5. Three tesla MR showed higher sensitivity than 1.5 T in diagnosing HCC (80.00% vs 57.69%, P = 0.015). Conclusion When the effect of field strength was eliminated, LI-RADS v2018 demonstrated high specificity but suboptimal sensitivity in distinguishing HCC from non-HCC primary liver carcinomas. Most iCCAs were categorized as LR-M or LR-TIV (may be due to non-HCC malignancy). However, nearly half of cHCC-CCAs were assigned as LR-5.