Mafic microgranular enclaves (MMEs), commonly found in granitoid intrusions, can provide unique perspectives on the nature of magma sources and evolution, physicochemical properties of magmas, and geotectonic dynamic evolution. However, their origin and generation remain under debate. In this paper, the Cretaceous Tongkeng pluton with MME occurrence located in the Xiaojiang area of Zhejiang Province, SE China, was examined. Zircon U-Pb dating indicates that the gabbroic diorite, MMEs, and their host quartz diorite all crystallized at 107–106 Ma. All samples from the Tongkeng pluton show a comparable range of initial ⁸⁷Sr/⁸⁶Sr values (0.70746–0.70841), ε_Nd(t) values (−4.9 to −2.9), and zircon ε_Hf(t) values (−7.3 to −2.9) with the peak value of −6 to −4. In addition, Pb isotope compositions are fairly consistent. Petrology, geochemical and isotopic compositions, and geochemical modeling suggest that the gabbroic diorite, MMEs, and their host rock were cognate and their primary magma was derived from the mixing between a mantle-derived magma and a crustal magma. The “magma differentiation and convection” model, proposed in this paper to improve our understanding of the origin of the MMEs and their host rock, suggests that the gabbroic and quartz dioritic magmas were formed by cognate magma differentiation, and the MME magma is a portion of the gabbroic dioritic magma that is incorporated into and mingled with the quartz dioritic magma.Misjudgment in the origin and generation of MMEs leads to an erroneous understanding of mantle properties, the genesis of granitoids, and therefore, many other geological processes. Hence, caution is needed when considering the relationship between the host granitoid and its associated MMEs with similar chemical and isotopic compositions, particularly for those exposed in areas where mafic rocks are absent (or undiscovered).