Objective To study the diagnostic value of magnetic resonance imaging (MRI) and spiral CT in thyroid microcarcinoma (TMC), in order to improve the diagnostic accuracy of TMC. Methods The preoperative imaging manifestations of MRI and spiral CT in 68 TMC patients who were confirmed by surgical pathology were retrospectively analyzed, and the diagnostic accordance rates were compared between the independent and the combined diagnosis. Results The diagnostic accordance rates of MRI and spiral CT in TMC were 73.53%(50/68) and 66.18%(45/68). The diagnostic accordance of combined MRI and spiral CT in TMC was 88.24%(60/68). The diagnostic accordance rate of combined MRI and spiral CT was significantly higher than that of independent examine, and there was statistical difference (P<0.05). The lesion detection rate of MRI was significantly higher than that of spiral CT:95.59% (65/68) vs. 83.82% (57/68), but the calcification lesion detection rate of spiral CT was significantly higher than that of MRI: 85.42% (41/48) vs. 4.17% (2/48), and there were statistical differences (P<0.05 or <0.01). There were no statistical differences in the detection rates of irregular shape lesions, boundary indistinct/coarse lesion, signal/uneven density lesions and cervical lymph node metastasis between MRI and spiral CT (P>0.05). Conclusions Spiral CT is superior to MRI in the micro-calcification detection, and MRI, with a high resolution of soft tissue, can display the lesions of surrounding tissue organs and neck lymph node metastasis better. The combined examine can increase the diagnostic accuracy of TMC.