To establish shear-wave elastography (SWE) combined with contrast-enhanced ultrasound (CEUS) algorithm (SCCA) and improve the diagnostic performance in differentiating focal liver lesions (FLLs). We retrospectively selected patients with FLLs between January 2018 and December 2019 at the First Affiliated Hospital of Sun Yat-sen University. Histopathology was used as a standard criterion except for hemangiomas and focal nodular hyperplasia. CEUS with SonoVue (Bracco Imaging) and SCCA combining CEUS and maximum value of elastography with < 20kPa and > 90kPa thresholds were used for the diagnosis of FLLs. The diagnostic performance of CEUS and SCCA was calculated and compared. A total of 171 FLLs were included, with 124 malignant FLLs and 47 benign FLLs. The area under curve (AUC), sensitivity, and specificity in detecting malignant FLLs were 0.83, 91.94%, and 74.47% for CEUS, respectively, and 0.89, 91.94%, and 85.11% for SCCA, respectively. The AUC of SCCA was significantly higher than that of CEUS (P = 0.019). Decision curves indicated that SCCA provided greater clinical benefits. The SCCA provided significantly improved prediction of clinical outcomes, with a net reclassification improvement index of 10.64% (P = 0.018) and integrated discrimination improvement of 0.106 (P = 0.019). For subgroup analysis, we divided the FLLs into a chronic-liver-disease group (n = 88 FLLs) and a normal-liver group (n = 83 FLLs) according to the liver background. In the chronic-liver-disease group, there were no differences between the CEUS-based and SCCA diagnoses. In the normal-liver group, the AUC of SCCA and CEUS in the characterization of FLLs were 0.89 and 0.83, respectively (P = 0.018). SCCA is a feasible tool for differentiating FLLs in patients with normal liver backgrounds. Further investigations are necessary to validate the universality of this algorithm.