Microbial-induced calcite precipitation (MICP) is a novel ground improvement method to increase the strength and stiffness of sand. However, the influences of temperature load on the internal microstructure of microbial cemented sand (MCS) material under the experimented strain have always been a key concern for the extensive application. Three kinds of experiments, X-ray diffraction (XRD), X-ray computed tomography (XCT), and scanning electron microscopy (SEM), were conducted to explore the composition, shape, and bonding characteristics of physical assemblies in this paper. A precision DEM modelling of MCS, mainly composed of irregular particle modelling and a mesoparameter calibration algorithm, has been proposed for the thermal cracking analysis under various strains (i.e., 1.0‰–3.0‰). Research results indicate that three kinds of bonding (that is sand-calcite, calcite-calcite, and sand-sand) are present in the MCS material. The application of temperature has a superposition effect on the damage of MCS material with increasing strain. Moreover, as the heating duration gradually increases, the effect of thermal rupture produces a distinct quiet period. The length of thermal cracks in the transverse direction increases throughout the heating process.