This study aimed to investigate the maternal factors and utilization of maternal care services associated with infant feeding practices in rural areas of Southern Nepal. Data from a cluster randomized controlled trial ‘MATRI-SUMAN’(Maternal Alliance for Technological Research Initiative on Service Utilization and Maternal Nutrition) conducted between 2015–2016 were analyzed. A total of 426 pregnant women in their second trimester were recruited from the MATRI-SUMAN trial, which was conducted on six villages in rural areas of the Dhanusha district, Nepal. A total of 379 mothers that had ever breastfed their infants, and followed for at least seven months after birth were included in the analysis. Multivariate logistic regression analysis was used to identify independent risk factors associated with child feeding practices after controlling for potential confounders. Of the 379 mothers, 41.4%, 53%, and 43% initiated breast feeding within the first hour of birth (EIBF), practiced exclusive breastfeeding (EBF), and initiated timely complementary feeding (CF) at six months, respectively. Multiple logistic regression results revealed that maternal education (secondary or higher), an occupation in the service/business/household sectors, receipt of MATRI-SUMAN intervention, more than four ANC (antenatal care) visits, and delivery in a health facility were associated with higher odds ratios of EIBF. Similarly, mothers with a primary, secondary and higher level of education, that worked in the service/business/household sectors, primiparous mothers, those that received MATRI-SUMAN intervention, visited ANC more than four times, and made a PNC (postnatal care) visit had higher odds ratios of EBF, while mothers who were 35–45 years of age were less likely to have used EBF. In addition, education to the secondary or a higher level, a male baby, receipt of MATRI-SUMAN intervention and a PNC visit had higher odds ratios of CF initiation at six months. The promotion of maternal ANC visits, birth at a health institution, and postnatal visits should be recommended in order to improve child feeding practices in Nepal.