Stroke patients with autonomic dysfunction are more likely to develop cardiac problems, which have been linked to lower functional outcomes and increased mortality. In this study, heart rate variability (HRV) detection paired with the Clinical Feature Scale will be utilized to elucidate the immediate impact of manual acupuncture on autonomic dysfunction of varying severity in the convalescence stroke phase. This is a randomized, single-blind, controlled clinical trial approach. At a ratio of 1:1, 60 appropriate patients will be randomly randomized into either the experimental or control group. On the basis of symptomatic treatment drugs, the experimental group will additionally undertake acupuncture therapy 3 times a week for 4 weeks, for a total of 12 times. Primary outcomes include 24-hour HRV and 60-minute HRV detection at week 4 compared with baseline. The secondary outcome is the score of clinical feature scale at week 4 compared with the baseline. Adverse events and safety indices will be recorded throughout the experiment. The SPSS V.25.0 statistical program was applied for analysis, and measurement data were expressed as mean ± SD.