this study was to discuss the application value of the embedded intelligent fetal heart rate monitoring system (EI system) based on empirical mode decomposition (EMD) algorithm in the monitoring of pregnant women with pregnancy bacterial infection complications, aiming to provide a reference basis for timely nursing of pregnancy bacterial infection complications. In this study, the blind source separation method was introduced to denoise the screened intrinsic modal function (IMF) components based on the EI system and the EMD algorithm. The signal to noise ratio (SNR) based on the EMD optimization algorithm was compared with that of other algorithms. Two hundred and sixty‐eight pregnant women in the obstetric clinic were selected as the research objects and divided into an observation group (abnormal fetal heart rate) and a control group (normal fetal heart rate). The pregnant women in both groups accepted the conventional nursing methods, and the EI system was adopted to monitor the fetal heart rate. The probability of abnormal fetal heart monitoring of pregnant women in observation group and control group was analysed. At the same time, the probability of bacterial infection complications was analysed. It was found that the EI system based on EMD algorithm showed obviously higher SNR in contrast to other algorithms. The waveforms of fetal heart monitoring in the observation group and the control group were significantly different (χ2 = 11.215, p < 0.05); microscopic examination of pregnant women secretion in the bacterial infection group revealed the presence of a large number of pathogenic bacteria; it was found that the infection rate of vaginosis was significantly different between the control group and the observation group (p < 0.01); there was a significant difference between the observation group and the control group in the complication of premature rupture of fetal membrane caused by bacteria (χ2 = 11.2, p < 0.01). In conclusion, the EI system based on the EMD algorithm could be undertaken as a tool for the preliminary diagnosis of pregnancy bacterial infection complications in pregnant women, which provided relevant basis for later nursing.