As China advances the construction of an independent knowledge system for philosophy and social sciences with Chinese characteristics, comprehensive social science journals are in a prime position to play a distinctive role. With their multidisciplinary scope and thematic openness, these journals are expected to integrate diverse academic resources, facilitate cross-disciplinary dialog, and engage with real-world issues. However, these journals have long been constrained by structural dilemmas, including the tension between disciplinary breadth and thematic depth, the homogenization of columns coupled with weakened academic impact, and a vicious cycle in which the loss of high-quality submissions further erodes journal competitiveness. These interrelated challenges have made it increasingly difficult for such journals to transition toward high-quality development. Based on years of editorial practice and case-based analysis, this study adopts a combination of systematic analysis and case study methods to explore how comprehensive social science journals can achieve systemic transformation in the new era. It systematically analyzes three major challenges: the structural contradiction between broad disciplinary coverage and thematic focus; the dual constraints of column homogenization and weakened academic impact; and the vicious cycle of manuscript loss and declining competitiveness. This study further investigates the underlying causes of these challenges, including the failure to accurately align with national cultural strategies, insufficient responsiveness to major national demands, and the lack of leadership in academic frontier innovation. In response, drawing on the practical experiences of representative journals, this paper proposes four pathways for transformation. First, the journals can strengthen political leadership by translating policy orientations into substantive academic themes, thereby integrating ideological work with knowledge production. Second, they can drive theoretical innovation by organizing interdisciplinary special issues around major social issues, thereby promoting a problem-centered knowledge model and drawing on the strengths of multiple fields. Third, by refining homegrown academic concepts grounded in Chinese practice, the journals can contribute to the development of a distinctive Chinese knowledge system. Fourth, by cultivating a sustainable academic community through intergenerational transmission, emerging scholars can be supported while engaging established experts to ensure a sustained flow of intellectual vitality. In these ways, comprehensive social science journals can effectively enhance their academic distinctiveness, content quality, and academic impact, thereby gradually overcoming the long-standing challenges. This study offers a systematic account of the core bottlenecks, transformation directions, and practical mechanisms for the high-quality development of comprehensive social science journals, providing both theoretical insights and actionable references for the same type of journal and contributing to the broader effort to develop China's independent knowledge system through high-quality academic publishing.