Under the macroscopic background of the in-depth implementation of the rural revitalization strategy and the accelerated transformation of the urban–rural dual structure, the issue of mental health of children in rural areas has risen to become a core topic concerning social fairness, justice, and sustainable development. This study is based on the dual theoretical framework of social ecosystem theory and cognitive-behavioral theory and adopts a mixed research paradigm that combines quantitative research and qualitative research to systematically deconstruct the mental health status and influencing mechanisms of children in rural areas. It conducts an empirical assessment of the intervention efficacy of social work services. The research was conducted in the two cities of Z and B in Province H. Through stratified random sampling, 600 children in difficult situations (including left-behind children, factually unsupported children, children from low-income families, and disabled children) were selected as the research sample and underwent standardized mental health assessments. The research method system exhibits a multi-complex feature. Quantitative research dimension: Relying on standardized psychological assessment tools, conduct quantitative analysis of the mental health level of the sample population; Qualitative research dimension: The study makes comprehensive use of in-depth interviews, participatory observation, and qualitative analysis of service archives, etc., to evaluate the practical effectiveness of social work services, Particularly for high-risk children with severe psychological trauma, suicidal tendencies, or self-abusive behaviors, structured interview techniques were adopted to construct a deep cognitive map of their psychological state and needs, in order to precisely capture the spectrum of mental health problems of special disadvantaged children and provide targeted basis for service optimization. The research results indicate that the psychological health problems of rural disadvantaged children exhibit multi-dimensional characteristics. Among them, emotional disorders (anxiety and depression) and social withdrawal account for a relatively high proportion, and the problem of low self-efficacy is particularly prominent. The mental health risks of children are influenced by the interaction of three factors: family (the lack of guardianship ability and the breakdown of parent-child connection), school (the absence of psychological support from teachers), and community (the scarcity of public service resources). Social work services have significant effects in enhancing individual resilience and building social support networks. However, there are issues such as insufficient service coverage, limited intervention duration, and the absence of cross-system collaboration mechanisms. The study proposes the following countermeasures: first, establish a “home–school–community–government” collaborative mental health service system, and incorporate social work services into the framework of rural children’s welfare policies; second, develop a long-term service mechanism centered on children, based on families as the foundation, and community as the carrier, with a focus on strengthening family function restoration and community resource integration; third, improve the evaluation standards of social work services and construct a multi-dimensional evaluation model that includes process indicators, output indicators, and impact indicators. This study not only provides empirical evidence for optimizing the mental health service system for rural disadvantaged children but also offers a reference path for the methodological innovation of social work intervention in the field of children’s welfare.