Although micrites (abiotic limestone) and thrombolites (typical biotic limestone), according to the sedimentation and biological action, can be primarily distinguished from intuitively field observation and rock slices analysis. However, further analysis of thermal decomposition unique characteristics to distinguish them has rarely been reported. Here, the comparative studies of thermal decomposition behavior between micrites and thrombolites were carefully investigated using thermogravimetric analyzer in nitrogen atmosphere at multi-heating rates of 5, 10, 20 and 30 K min−1 from 323.15 to 1273.15 K. Moreover, the mineralogical compositions were both analyzed by powder X-ray diffraction followed by the results of calcite acting as the basic constituent for further verified. The kinetic model function and kinetic parameters were calculated by Flynn–Wall–Ozawa, Kissinger–Akahira–Sunose and Popescu methods, respectively. The results showed that the kinetic parameter activation energy (E) of thrombolites was obviously higher than that of micrites, which suggests the former have a higher crystallinity. In addition, the results of difference significance analysis showed extremely significant differences (P < 0.01) via statistical analysis using SPSS v19.0 for the E values between micrites and thrombolites calculated by different methods. These above results further confirmed that the thermal stability and crystallinity of thrombolites were obviously higher under the inducing effects by typical microorganisms. This provided very important useful information for understanding the mechanisms of abiotic and biotic limestones formed in nature; in particular, the thermal analysis of thrombolites maybe also provides an important guiding significance for both indoor and outdoor similar studies.