Introduction: It is challenging to diagnose liver masses in the context of a rough liver background using computed tomography and magnetic resonance imaging. Perfluorobutane CEUS microbubble, an ultrasound (US) contrast agent, has a unique phase called the Kupffer phase. This study aimed to explore whether the diagnostic ability of Kupffer-CEUS is affected by the rough liver background. Methods: A prospective analysis was conducted on patients with access to histological pathology of FLLs and liver parenchyma from 23 centers between August 2020 and March 2021. Kupffer-CEUS was performed on 552 patients, who were divided into two groups (normal and abnormal) based on the pathological results of liver parenchyma, and the abnormal group was further divided into four groups (sight liver fibrosis, serious liver fibrosis, fatty liver, mixed). Kupffer-CEUS was divided into vascular phase and vascular and Kupffer phase. Results: In Kupffer-CEUS, differences in diagnostic efficiency of FLLs between normal and abnormal liver backgrounds were not statistically significant. However, in patients with abnormal liver backgrounds, the specificity (57.45% vs. 74.47%, p = 0.008) and accuracy (89.81% vs. 96.92%, p < 0.001) of the vascular phase in distinguishing malignant from benign lesions were statistically lower than those of the vascular and Kupffer phase (V&KP). Subgroup analysis revealed that the sensitivity, specificity, and accuracy of V&KP in screening FLLs were all higher than those of vascular phase, except for the accuracy in patients with serious liver fibrosis (98.51% vs. 94.06, p < 0.001). Conclusion: This study indicated that although there is no obvious restriction on the choice of Kupffer-CEUS methods when diagnosing liver masses in patients with normal or abnormal liver backgrounds, Kupffer phase CEUS can effectively reduce the misdiagnosis of FLLs. Particularly for patients with serious liver fibrosis, contrast-enhanced US combined with the Kupffer phase can provide a more accurate diagnosis than conventional contrast-enhanced ultrasonography.