Objective To explore the effects of exercise instruction during the whole course of pregnancy by mobile phone APP on master of pregnancy motor knowledge, body movement during pregnancy and gestation related index. Methods Totals of 186 pregnant women who received prenatal examination during early pregnancy were selected. They were divided into intervention group (n=96) and control group (n=90) according to random number table. Patients in the intervention group received exercise instruction during the whole course by mobile phone APP involving pushing pregnancy motor knowledge at regular intervals, sharing authoritative movement method, reminding the time of further consultation and arranging experts for response to messages of pregnant women and so on. Patients in the control group accepted routine exercise instruction with the existing model of pregnancy movement. The master of pregnancy motor knowledge, body movement during pregnancy and gestation related index were compared. Results The total scores of the master of pregnancy motor knowledge in the intervention group and the control group were (77.22±7.07) and (63.31±5.91) with a significant difference (t=14.592, P< 0.001). There was a statistically significant difference in the average total energy consumed per week between the intervention group (154.62±20.74) MET-hours and the control group (105.48±15.81) MET-hours (t=18.240, P< 0.001). Besides, the differences in pregnancy weight gain, antenatal weight, postpartum BMI and pelvic floor muscle strength between two groups were significant (t=-7.715, -4.438, -9.805, 13.988; P< 0.001). The amount of vaginal bleeding, cesarean section rate, perineotomy rate with spontaneous labor during the second stage, total stage of labor and two hours after delivery in the intervention group were lower than those in the control group with significant differences (P< 0.05). Conclusions The exercise instruction during the whole course of pregnancy by mobile phone APP can improve the master of pregnancy motor knowledge and increase the energy consumed during pregnancy, so as to improve the gestation related index, reduce the cesarean section rate and perineotomy rate with spontaneous labor. It is better than the existing model of pregnancy movement.