Objective To investigate the clinical application value of 99Tcm-MIBI SPECT/CT fusion imaging in classifying brain tumor of malignant and benign, and compared with pure SPECT imaging or pure CT imaging, further highlight the clinical application value of 99Tcm-MIBI SPECT/CT fusion imaging. Methods Forty-five patients with suspected brain tumor underwent 99Tcm-MIBI SPECT imaging, CT imaging and 99Tcm-MIBI SPECT/CT fusion imaging. The sensitivity, specificity and accuracy of the above three methods were calculated separately for brain tumor with postoperative pathologic results as the standard and analysis the results of single imaging and fusion imaging respectively by the methods of statistical. Results Compared with the pure SPECT imaging, there was a statistically significant difference of sensitivity (2=4.383, P<0.05) , specificity(2=3.949, P<0.05) ,accuracy (2=8.073, P<0.01) of SPECT/CT fusion imaging. Compared with the pure CT imaging, there was a statistically significant difference of sensitivity (2=5.543, P<0.05), specificity (2=5.100, P<0.05), accuracy (2=10.497, P<0.01) of SPECT/CT fusion imaging. Conclusion Compared with single imaging, 99Tcm-MIBI SPECT/CT fusion imaging has more diagnostic value in the diagnosis of brain tumor.