The disposal of bauxite tailings (BT) remains a significant challenge for the global aluminum industry. However, its application in Limestone Calcined Clay Cement (LC3) systems shows immense potential. Despite this, the optimal calcination temperature for BT and its effects on LC3 performance have yet to be clearly defined. To address this gap, the study employs thermogravimetric (TG) analysis, X-ray diffraction (XRD), Fourier-transform infrared (FTIR) spectroscopy, R3 reactivity tests, hydration heat measurements, and backscattered electron (BSE) imaging to systematically investigate the relationship between calcination temperature, raw material properties, and LC3 performance. The results reveal that, in contrast to the conventional calcination temperature of 800 °C typically used for clay materials, calcining BT at 600 °C achieves complete dehydroxylation of kaolinite, while balancing amorphous content, degree of polymerization, and pozzolanic activity. Under these conditions, the 28-day compressive strength reaches 43.7 MPa, significantly exceeding that of samples calcined at other temperatures and the P·I 42.5-grade benchmark cement. This performance improvement is primarily attributed to a substantial increase in the content of C-(A)-S-H and AFm phases (Hc/Mc), along with more uniform hydration reactions and tighter particle bonding around unhydrated particles, resulting in a robust matrix structure. Based on these findings, future research should focus on the microstructural properties of the phases surrounding particles in LC3 systems incorporating low-grade clays. Such an approach could more efficiently and directly determine the optimal calcination temperature, minimizing reliance on indirect performance indicators. This study not only provides a scientific foundation for the application of bauxite tailings in LC3 systems but also offers new insights for promoting low-carbon cement in regions with limited clay resources, contributing to the sustainable development of both construction materials and the aluminum industry.