Polyoxometalates (POMs) are mineral nanoclusters with many advantages in various diagnostic fields, in particular cancer detection. This study aimed to synthesize and evaluate the performance of gadolinium–manganese–molybdenum polyoxometalate (Gd-Mn-Mo; POM) nanoparticles coated with chitosan–imidazolium (POM@CSIm NPs) for detecting 4T1 breast cancer cells by magnetic resonance imaging in vitro and in vivo. The POM@Cs-Im NPs were fabricated and characterized by FTIR, ICP-OES, CHNS, UV–visible, XRD, VSM, DLS, Zeta potential, and SEM. Cytotoxicity, cellular uptake, and MR imaging in vivo and in vitro of L929 and 4T1 cells were also assessed. The efficacy of nanoclusters was demonstrated using MR images of BALB/C mice bearing a 4T1 tumor in vivo. The evaluation of the in vitro cytotoxicity of the designed NPs showed their high biocompatibility. In fluorescence imaging and flow cytometry, NPs had a higher uptake rate by 4T1 than L929 (p < 0.05). Furthermore, NPs significantly increased the signal strength of MR images, and its relaxivity (r1) was calculated as 4.71 mM−1 s−1. MR imaging also confirmed the attachment of nanoclusters to cancer cells and their selective accumulation in the tumor region. Overall, the results showed that fabricated POM@CSIm NPs have considerable potential as an MR imaging nano-agent for early 4T1 cancer detection.