Superparamagnetic iron oxide nanoclusters (SPIONs) modified with pH (low) insertion peptide (pHLIP) could be advantageous for magnetic resonance imaging (MRI) diagnosis of liver tumors at the early stage due to their unique responsiveness to the tumor acidic microenvironment when tumor markers are unknown. However, many critical aspects including the effectiveness of selective MRI in liver tumors, types of delivery and the potential safety profile in cirrhosis need to be fully evaluated. In this study, we report the evaluation of non-targeting, C- or N-pHLIP modified SPIONs as the contrast agent for selective MRI of liver tumors and their potential toxicity profile in cirrhosis. It was found that N-pHLIP modified SPIONs did not result in the loss of liver tumor in the T2-weight MRI but provided additional dynamic details of tumor structures that would enhance the diagnosis of liver tumors at a small size below 8 mm. In addition, an enhanced safety profile was found for N-pHLIP modified SPIONs with almost fully recoverable impact in cirrhosis. In contrast, the poly-D-lysine assembled SPIONs and C-terminus linked pHLIP SPIONs had non-tumor specific MRI contrast enhancement and potential safety risks in cirrhosis due to the iron overload post injection. All these results implied the promising potential of N-terminus linked pHLIP SPIONs as an MRI contrast agent for the diagnosis of liver tumors.