Objective To investigate the early motor development and the risk factors affecting motor development in children with congenital muscular torticollis (CMT) aged 0–3 months. Methods CMT infants admitting to the Department of Rehabilitation Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine between January 1st, 2016 and April 30th, 2018 were enrolled as CMT group, and contemporaneous age-matched healthy infants were enrolled as the control group. Motor development was assessed with the Alberta Infant Motor scale (AIMS). We collected the birth weight, birth length, mode of birth, sleep position, and prone time when awake as dependent variables, and used multiple linear regression to find the variables that had significant effect on AIMS scores. Results There were 97 CMT infants (62 males and 35 females) with the mean age of (46.8±17.3) days, mean birth weight of (3.34±0.38) kg and mean birth length of (49.56±0.93) cm in the CMT group, while there were 97 healthy infants (60 males and 37 females) with the mean age of (45.1±19.4) days, mean birth weight of (3.38±0.35) kg and mean birth length of (49.84±1.03) cm in the control group, and the differences in sex, age, birth weight, birth length between the two groups were not statistically significant (P>0.05). AIMS centiles showed that 36 infants (37.1%) in CMT group had suspicious or abnormal motor development, while only 12 infants (12.4%) in the control group had; there was a significant statistical difference between the two groups (χ2=15.945, P<0.001). Multiple linear regression analysis showed that the time of prone position when awake and CMT had significant influence on the AIMS scores (F=64.851, P<0.001). Infants who had a long prone position when awake had significantly higher AIMS scores and CMT had a significantly lower AIMS scores (P<0.001). Conclusions The risk of early motor retardation in infants with CMT aged 0–3 months is higher than that in healthy infants of the same age. The decrease in prone position when awake and CMT may be the causes of delayed motor development. Clinical medical personnel and family caregivers should pay more attention to motor development and provide reasonable intervention to CMT infants.