Objective To compare the clinical value of renal artery ultrasound hemodynamic parameters and non-enhanced magnetic resonance in evaluating renal artery stenosis and anatomical abnormalities. Methods A total of 149 patients with chronic kidney disease(CKD) were enrolled. Renal artery stenosis and anatomical variations were evaluated by non-enhanced renal artery magnetic resonance angiography (NEC-MRA). Color Doppler ultrasound was used to detect hemodynamic parameters of each segment of the renal artery. Renal function assessment was conducted through two methods: radionuclide renal dynamic imaging and the calculation of the estimated glomerular filtration rate (eGFR) using the CKD Epidemiology Collaboration (CKD-EPI) study equation formula. Results Among the 149 patients in this study, 17 cases (11.4%) were at CKD stage 1, 39 cases (26.2%) at stage 2, 44 cases (29.5%) at stage 3, 17 cases (11.4%) at stage 4, and 32 cases (21.5%) at stage 5. The resistance index (RI) of patients with initial renal artery stenosis was significantly higher than that of patients without stenosis (P=0.000), while there was no statistically significant difference in peak systolic velocity (PSV) (P= 0.443). There was no statistical difference in PSV and RI between the two groups with or without midstream stenosis (P=0.190, P=0.088). There was no significant difference in PSV and RI between the initial and middle segments of the anatomical variation group and the non-variation group (P > 0.05). The eGFR on the non-stenotic side of the initial segment of the renal artery was significantly higher than that on the stenotic side (Z=2.98, P=0.029), and eGFR on the non-stenotic side in the middle segment was significantly higher than that on the stenotic side (Z=4.025, P=0.001). There was no statistical difference in eGFR between the anatomical variant side and the non-variant side (Z=0.579, P=0.550). Conclusions Color Doppler ultrasound PSV and RI show higher value in diagnosing initial renal artery stenosis than middle renal artery stenosis and have no diagnostic value for anatomic variation of renal artery. Both initial and middle renal artery stenosis leads to a decrease in the ipsilateral renal GFR, while variations in renal artery anatomy does not affect ipsilateral renal GFR.