Objective: The impact of maternal psychosocial stress on young children’s mental difficulties is unclear. This study investigated the joint effects of the socioeconomic status and parent-child relationships on emotional and behavioral difficulties in preschool children. Methods: The case-control study included 1416 mothers and their 4–6 year-old children pairs, living in Kaunas city, Lithuania. The parent-child relationships were measured using the Parent-Child Dysfunctional Interaction subscale. Children’s mental health difficulties were assessed by the Strengths and Difficulties Questionnaire. We used logistic regression models to indicate the strength of the associations. Results: Lower socioeconomic status women more often than higher ones reported pathological mother-child relations. Low education level was associated with statistically significant increase adjusted odds ratios for emotional symptoms and total behavioral difficulties. With reference to the group of better-educated mothers and normal mother-child relations, low education and pathological mother-child relations statistically significantly increased the risk of total difficulties in 4–6 year-old children; the adjusted odds ratios were 2.45; 95% CI 1.51–3.99. Conclusions: Pathological mother-child relations strengthened the effect of lower education on the increased risk of emotional and behavioral difficulties in preschool-age children. Measures oriented towards health behavior and psychosocial difficulties management may decrease children’s emotional and behavioral difficulties.