To solve the nanoparticles (NPs) agglomeration phenomena of nanometer calcium carbonate (nano-CaCO3) modified asphalt binder, in this paper, solvent-free CaCO3 nanofluids (NFs) were prepared based on surface-functionalized CaCO3 NPs to study the effect on asphalt. Microscopic structures, compositions, and thermal stability were characterized by Fourier transform infrared spectrometer (FTIR), X-ray diffractometer (XRD), transmission electron microscope (TEM), and thermogravimetric analyzer (TGA), respectively. Results showed that perfect CaCO3 NFs were successfully prepared, and were good enough for asphalt mixing due to their excellent thermal stability. Scanning electron microscopy (SEM), conventional tests, dynamic shear rheometry (DSR), and bending beam rheometry (BBR) were conducted to investigate the modifying effect. The SEM results indicated that CaCO3 NFs had better compatibility with asphalt binder than original CaCO3 NPs. Conventional and DSR test results demonstrated that CaCO3 NFs had slight negative effects on high-temperature performance while improving the low-temperature performance of the asphalt binder. The BBR test results confirmed that the modifier addition effectively enhanced asphalt binders’ low-temperature crack resistance performance.