A unique feature of cordierite is the negative thermal expansion of its c‐axis, while the a‐ and b‐axes show positive thermal expansion behavior. The thermal expansion mechanism of cordierite has been investigated in many theoretical studies, but the effect of Ti or Ge doping has not yet been studied theoretically. Here, we investigate the thermal expansion behavior of Ti‐ and Ge‐doped cordierite by ab initio molecular dynamics (AIMD) simulation. The computational cost of AIMD simulation for cordierite doped with Ti or Ge is challenging due to the many different configurations of crystal models. We overcame this computational difficulty by separating the respective models into groups with identical symmetry, then we performed MD simulation for each different symmetry crystal model. To understand the mechanism of the negative thermal expansion of the c‐axis, we investigated the changes in all the bond lengths and angles. We found that the negative thermal expansion of the c‐axis is coupled with the increase in the O–Al–O angle and the shrinkage of the O–Si–O angle at the T1 site in cordierite, which suggests the rotation of the six‐membered ring. This study provides insight into the mechanism of thermal expansion of cordierite with Ti and Ge doping. Moreover, the approach presented here can be generally applied to investigate the thermal expansion behavior of other ceramic materials within reasonable accuracy and computational cost.