Porphyry deposits are globally the main source of copper and molybdenum, and their formation is related to the epigenetic emplacement of intermediate to felsic porphyry intrusions. The fine ore.forming processes and fertility assessments of porphyry deposits have been an important frontier since the beginning of this century. As the most common and chemically stable accessory minerals in intermediate to felsic rocks, zircon and apatite have been widely used in the study of magmatism and mineralization in recent years. On the one hand, this is due to the rapid progress and popularization of in.situ analysis technology represented by LA.ICP.MS in recent years, which makes it possible to accurately obtain information of mineral trace elements; on the other hand, the chemical composition of zircon and apatite contains rich diagenesis and mineralization information, including age, temperature, oxygen fugacity, water content, S and Cl content, etc. Combining these indicators can reveal the evolution and fine processes of magma.mineralization. This paper reviewed the main progress in the ore.forming processes and fertility assessments of porphyry deposits by zircon and apatite, especially in discriminating rock types, petrogenesis, magma sources, estimating parent magma composition, discriminating ore deposit types, tracing sources of ore.forming fluids, revealing fluid metasomatism and alteration zoning of porphyry deposits, quantifying post.mineralization exhumation and preservation. Furthermore, a summary of problems and challenges in the study is presented. Finally, some suggestions are proposed for the application of zircon and apatite in study of porphyry deposits in the future.