Objective To analyze the stress distributions of two root canal preparation shapes of oval root canals with micro-crack. Methods Twenty single-canal mandibular premolars with oval canals were expanded to create micro-cracks. Roots were sectioned after staining. The generation and distribution of dentin micro-cracks were observed under microscope. Then a finite element (FE) model of sectioned enlarged oval canal roots with micro-cracks was established. The stress distribution of micro-crack and root were analyzed under lateral loading. Results Cracks always appeared in the buccolingual sides of oval canal roots and extended from the intracanal wall to the root surface. This was consistent with the stress concentration on the buccolingual side of the root canal wall shown by FE analysis. When micro-cracks occurred, stresses were transferred to the crack tip and the peak values increased sharply nearly 5 times. This made the cracks propagate easily along this direction, especially in the long axis direction of the tooth. Conclusions The presence of micro-cracks does not change the general stress concentration on root with two preparation morphologies of oval canals. However, the micro-crack causes an extreme stress concentration in the crack tip. This may be the mechanism of rapid propagation of microcracks into vertical root fracture, and dentists need to pay high attention.