Background Constipation is one of the common symptoms in childhood. The prevalence of FC is about 0.5–32% and still on the rise according to global statistics. The aim of this study is to explore the associations between family-related factors (e.g., parental conflict, parenting style, and parent-child relationship) and functional constipation of preschool children based on family system theory. Methods The study is a case-control survey of preschoolers in China. In total, 108 preschoolers with functional constipation diagnosed with pediatric Rome IV criteria and 324 healthy examination preschoolers without functional constipation were enrolled in the study. Parents completed the following 5 instruments: General information questionnaire, the Parental Conflict Scale, the Parenting Style Questionnaire, the Child-parent Relationship Scale and the Children's Emotional Adjustment Scale-Preschool Version. Results Nine categories of factors which significantly predicted functional constipation in preschoolers were retained in the final logistic regression model: Second child in birth order (OR = 0.456; 95% CI, 0.229 to 0.910), children picky eating (OR = 2.936; 95% CI, 1.133 to 7.611), bad bowel habits (OR = 2.896; 95% CI, 1.391 to 6.028), parental history of constipation (OR = 3.259; 95% CI, 1.600 to 6.639), parents blaming the child for having a bad bowel movement (OR = 3.788; 95% CI, 1.391 to 10.318), more than 3 hours of fathers-child interaction time per day (OR = 0.137; 95% CI, 0.024 to 0.778), parental conflict (OR = 1.981; 95% CI, 0.950 to 3.831), doting or authoritarian family style (OR = 1.644; 95% CI, 1.067 to 2.534, OR = 2.481; 95% CI, 1.362 to 4.519), and anxiety control or temper control in children (OR = 0.492; 95% CI, 0.303 to 0.799, OR = 0.189; 95% CI, 0.103 to 0.348). Conclusions This study identified the significant associations between family-related factors and functional constipation in preschool children, which provide implications for healthcare professionals to address functional constipation in early childhood using a preventive lens.