Background: Some adverse pregnancy outcomes are rooted in the gestation period and can influence the mother, newborn, or both. This study aimed to investigate the prevalence of pregnancy complications and their relationship with neonatal complications in mothers visiting healthcare centers in Zahedan, Iran. Methods: This cross-sectional study was conducted on 630 women visiting health care centers in Zahedan selected using systematic random sampling. Demographic information and anthropometric indices were collected and recorded in gestational and neonatal care forms. The data were analyzed in SPSS v. 22 using the chi-square test. Results: The results revealed that 18.9% of the mothers had anemia, 12.7% gestational diabetes mellitus (GDM), 5.1% thyroid disorders, 4% hypertension, and 2.1% preeclampsia. Moreover, 14.1%, 41.1%, and 22.7% of the mothers were underweight, overweight, and obese, respectively. A significant relationship existed between the infant's birth weight and the mother's body mass index, hypertension, GDM, and maternal iron deficiency anemia (P < 0.05). Infant jaundice was also significantly related to GDM and preeclampsia (P < 0.05). Conclusions: Identifying problems threatening the health of mothers and newborns and paying more attention to nutritional health care during pregnancy are efficient strategies for preventing and controlling pregnancy-related neonatal complications and the health of mothers and newborns. Specific attention to prevention programs, strengthening health care policies during pregnancy, and promoting prenatal care and self-care are major health priorities.