In this investigation, a functionalized SiO2 nanofluid was developed by integrating sodium oleate to mercapto-terminated nano-SiO2 via the thiol-ene “click” reaction. The developed nanofluid in the presence of higher concentrations (> 40,000 ppm) of NaCl at 70 °C was confirmed to be more stable than the original SiO2 nanofluid based on the outcomes obtained from precipitate observation, particle dimension, and zeta potential measurements. Successful integration of sodium oleate on the target nanoparticles was corroborated by a series of characterization approaches. Furthermore, the viscosity, contact angle, and interfacial tension (IFT) determinations were conducted to investigate nanofluids' potential for enhanced oil recovery (EOR). The results indicated that the viscosity of the functionalized SiO2 nanofluid (labeled FF-4) accounted for 3.48 cp after adding 40,000 ppm NaCl, while that of the original SiO2 nanofluid (labeled OF-4) was 1.15 cp. From the contact angle values, the carbonate rock surface was transformed from oil-wet (135°) to water-wet (72° and 38°) after being treated with the OF-4 and FF-4. The wettability alteration was attributed to the formation of the wedge film in the contact line area between the rock and fluids (oil sample and nanofluid). The functionalized nano-SiO2 helped to reduce IFT because of the simultaneous presence of the alkane chain (oleophilic) and carboxylate group (oleophobic) on the particle surface, making the functionalized nano-SiO2 have an amphiphilic structure. However, the original nano-SiO2 hardly changed IFT. Micro-model experiments showed that the OF-4 had a prominent oil displacement effect by changing wettability to a water-wet state and reducing the viscous fingering phenomenon. Core flooding tests demonstrated that the oil recovery factor of the FF-4 was almost 2.5 times that of the OF-4. Viscosity improvement was considered as a new oil recovery mechanism after wettability alteration and IFT reduction. This paper revealed the important properties of the functionalized nano-SiO2 and provided a novel efficient nanofluid for EOR in carbonate reservoirs.