The relationship between the thickness of surface molecularly imprinted polymers (MIPs) and specific recognition performance of transferrin (Trf) as well as the quantitative relation between the grafting amount of Mn-ZnS room-temperature phosphorescence (RTP) quantum dots (QDs) (short for PQDs) and RTP signals for recognition of Trf was analyzed in this study. Based on analysis results, RTP protein mesoporous imprinting microspheres (SiO 2 −PQDs−MIPs) with high specificity and strong interference resistance were developed using a mesoporous SiO 2 nanomaterial that can create more three-dimensional precise recognition sites as the matrix and using PQDs with strong resistance to background fluorescence interference as the luminescent materials. A discriminatory analysis of Trf was realized by the phosphorescence quenching principle based on light quenching caused by the photoinduced electron transfer. The concentration range, limit of detection, relative standard deviation, and imprinting factor of Trf detection under pH 7.4 are 0.05−1.0 μM, 0.014 μM, 3.23%, and 3.09, respectively. Although the sensing signals of SiO 2 −PQDs−MIPs for proteins are based on the phosphorescence of PQDs, they are particularly suitable for specific recognition and accurate quantitative detection of proteins in biological fluids. Research conclusions are expected to realize high-efficiency recognition of target proteins in actual biological samples.