Objective To investigate the value of serum alpha-fetoprotein (AFP), alpha-fetoprotein-L3 (AFP-L3), and plasma heat shock protein 90 alpha (HSP90α) in the differential diagnosis of hepatitis B cirrhosis and hepatitis B virus-associated hepatocellular carcinoma (HBV-HCC), and to analyze the correlation between these markers and hepatitis B virus deoxyribonucleic acid (HBV-DNA) load. Methods A total of 102 patients with HBV-HCC (HBV-HCC group), 74 patients with hepatitis B cirrhosis (hepatitis B cirrhosis group), and 80 healthy individuals undergoing physical examination during the same period (healthy group) were enrolled from August 2022 to August 2025 at the General Hospital of Anyang Iron and Steel Group Co., LTD. from August 2022 to August 2025, together with 80 healthy individuals (healthy control group), were enrolled in the study. Serum AFP, AFP-L3, and HSP90α, as well as HBV-DNA load, were measured and compared among the three groups. Receiver operating characteristic (ROC) curves were constructed to evaluate the diagnostic value of the above serum markers for hepatitis B cirrhosis and HBV-HCC. The correlations between AFP, AFP-L3, HSP90α, and HBV-DNA load were also examined in patients with hepatitis B cirrhosis and HBV-HCC. Results The levels of AFP, AFP-L3, and HSP90α were higher in the HBV-HCC group than in the hepatitis B cirrhosis group and the healthy group, and were higher in the hepatitis B cirrhosis group than in the healthy group (all P<0.05). The HBV-DNA load was higher in the HBV-HCC group than in the hepatitis B cirrhosis group (P<0.05), while no HBV-DNA was detected in the healthy group. Combined detection of serum AFP, AFP-L3, and HSP90α showed better diagnostic performance for both hepatitis B cirrhosis (area under the curve [AUC]=0.930, 95%CI: 0.891-0.969) and HBV-HCC (AUC=0.904, 95%CI: 0.861-0.947) than any single marker, with high sensitivity (93.24%, 88.24%) and specificity (90.00%, 83.78%) (P<0.05). Pearson correlation analysis showed that in patients with hepatitis B cirrhosis, serum AFP, AFP-L3, and HSP90α levels were positively correlated with HBV-DNA load (r=0.721, 0.655, 0.784, P<0.05). The same positive correlations were also observed in patients with HBV-HCC (r=0.769, 0.587, 0.658, P<0.05). Conclusion Serum AFP, AFP-L3, and HSP90α have good diagnostic value in differentiating hepatitis B cirrhosis from HBV-HCC, and the levels of these three markers are significantly correlated with HBV-DNA load.