This study aims to detect early changes of kidney in patients with primary hypertension by 3.0 T functional magnetic resonance imaging (fMRI). 26 patients with primary hypertension (hypertension group) and 33 healthy volunteers (control group) underwent conventional and functional magnetic resonance scans, which included blood oxygen level-dependent (BOLD) MRI, diffusion weighted imaging (DWI) and diffusion tensor imaging (DTI). We measured renal cortical thickness (CT), parenchymal thickness (PT), and functional values of renal cortex and medulla including R2* value, apparent diffusion coefficient (ADC) value and fractional anisotropy (FA) value in each group, and then calculated the cortical/parenchymal thickness ratio (CPR). Compared with those in the control group, CT and CPR in hypertension group were larger (P<0.01), cortical and medullar R2* values increased (P<0.01) whereas medullar FA values decreased (P<0.05). It could be well concluded that noninvasive 3.0 T functional MRI would have important clinical significance in identifying early abnormalities of kidney in hypertension patients.