The non-specific adsorption of interferents onto the outside surface of molecularly imprinted polymers (MIPs) particles is disadvantageous for selective determination of the template molecules. Based on the fact that the responses of non-imprinted polymers (NIPs) and MIPs particles to non-template molecules are similar, the anti-interference ability of MIPs sensor can be much improved via differential strategy, demonstrated by bovine hemoglobin (BHb) determination. The MIPs for BHb were prepared via surface imprinting and sol-gel process, with graphene quantum dots@SiO2/CdTe quantum dots (GQDs@SiO2/CdTe QDs) for ratiometric fluorescence measurements. By using a weight factor of 1.283 to compensate the lower specific surface area in NIPs particles, the differential ratiometric fluorescence signals between MIPs and NIPs channels to 2.00 μM ovalbumin and phycocyanin are equivalent to BHb at the concentration of 0.025 and 0.014 μM, which are only about 11 % and 5.8 % of the interference level in the normal ratiometric fluorescence method, respectively. The differential ratiometric fluorescence measurement was also performed in a smartphone-based device for field analysis of BHb in urine samples, with the linear range of 0.05–4 μM and the detection limit of 13 nM.