Frascati criteria for diagnosis of HIV-associated neurocognitive disorder lacks sensitivity, specificity, susceptible to learning effect, socioeconomic position and other confounding factors. fMRI can sensitively discover pathophysiological changes in HIV-infected central nervous system. In our study, ALFF and fALFF separately well classified HIV-positive and HIV-negative groups with AUC = 0.65 and 0.62, respectively. Our findings of injured frontal,parietal and occipital cortex associated with execution and attention function were consistent with previous studies, indicating activations reduced in the frontal lobe but increased in occipital lobe among patients with HAND. Both ALFF and fALFF could be biomarkers for objectively classifying HIV individuals.