It is a challenge to differentiate multiple system atrophy parkinsonism (MSA-P), Parkinson's disease (PD), and progressive supranuclear palsy (PSP). We aimed to explore the value of external anal-sphincter electromyography (EAS-EMG) and urethral-sphincter electromyography (US-EMG) in differential diagnosis with MSA-P, PD, and PSP. A total of 149 subjects, including 27 MSA-P, 100 PD, and 22 PSP, were recruited. The average duration and amplitude of motor unit potentials (MUPs), percentage of polyphasic MUPs, amplitude during strong contraction, and recruitment pattern during maximal voluntary contraction were recorded. The differences in EAS-EMG and US-EMG results between MSA-P, PD, and PSP were analyzed. In EAS-EMG examination, the average duration of MUPs of MSA-P was significantly longer than that of PD and PSP; the percentage of polyphasic MUPs and the ratio of simple phase and simple-mix phase of MSA-P and PSP were significantly higher than that of PD; the amplitude during strong contraction of MSA-P was significantly lower than that of PD. In US-EMG examination, the average duration of MUPs in male MSA-P was significantly longer than that in male PD and PSP; the ratio of simple phase and simple-mix phase in male MSA-P was significantly higher than that in male PD; there was no statistical difference in US-EMG indexes between male PD and PSP male. And because only one female PSP was examined, only female MSA-P and PD were compared, the average duration of MUPs in female MSA-P was significantly longer than that in female PD; the ratio of simple phase and simple-mix phase in female MSA-P was significantly higher than that in female PD. The average duration of MUPs and the ratio of the simple phase and simple-mix phase of EAS-EMG and US-EMG all can provide the basis for the differential diagnosis between MSA-P and PD. US-EMG can be used as a supplement to differentiate MSA-P from PD when EAS-EMG is limited. The only discriminating indicator between MSA-P and PSP seems to be the average duration of MUPs of EAS-EMG and US-EMG. There is still a lack of diagnostic electromyography indicators between PD and PSP.