Objectives To investigate the differences in the pattern of striatal (caudate and putamen) dopamine transporter (DAT) loss in a multiple system atrophy (MSA) cohort, based on the clinical variants parkinsonian subtype (MSA‐P) and cerebellar subtype (MSA‐C) via (11)C‐N‐2‐carbomethoxy‐3‐(4‐fluorophenyl)‐tropane (11C‐CFT) positron emission tomography (PET) imaging. Materials and Methods One hundred and six subjects (forty‐one patients with probable MSA‐P; forty patients with probable MSA‐C; twenty‐five healthy controls) underwent 11C‐CFT PET. Subregional 11C‐CFT uptake of bilateral caudate, anterior putamen, and posterior putamen was calculated respectively to measure the striatal dopaminergic function. Results Significant decrease in DAT binding in striatum was revealed in patients with MSA‐C and MSA‐P compared to normal controls (all regions, MSA‐C vs controls, P < .0001; MSA‐P vs controls, P < .0001). DAT reduction was more pronounced in MSA‐P patients than that in MSA‐C patients (all regions, P < .0001). Eleven of forty MSA‐C patients displayed no DAT loss, whereas striatal DAT loss was evident in all MSA‐P patients. MSA‐P subtype showed a more obvious anteroposterior gradient of DAT loss and more asymmetric dopaminergic dysfunction compared to MSA‐C patients. Conclusion The subtypes of MSA studied here show significantly different spatial/anatomic patterns of striatonigral degeneration which may provide insights into their disease pathophysiology. Specifically, MSA‐P patients exhibit an uneven and much greater pronounced loss of dopamine innervation, while a relatively uniform pattern is revealed in patients with the MSA‐C. Furthermore, the typical reduction in DAT 11C‐CFT binding in striatum is not present in all MSA‐C patients, with a minority of cases showing normal DAT binding.