Check-dam construction is an effective and widely used method for sediment trapping in the Yellow River Basin and other places over the world that are prone to severe soil erosion. Quantitative estimations of the dynamic sediment trapped by check dams are necessary for evaluating the effects of check dams and planning the construction of new ones. In this study, we propose a new framework, named soil and water assessment tool-dynamic check dam (SWAT-DCDam), for modeling the sediment trapped by check dams dynamically, by integrating the widely utilized SWAT model and a newly developed module called DCDam. We then applied this framework to a typical Loess watershed, the Yan River Basin, to assess the time-varying effects of check dam networks over the past 60 years (1957–2016). The DCDam module generated a specific check dam network to conceptualize the complex connections at each time step (monthly). In addition, the streamflow and sediment load simulated by using the SWAT model were employed to force the sediment routing in the check dam network. The evaluation results revealed that the SWAT-DCDam framework performed satisfactorily, with an overestimation of 11.5%, in simulating sediment trapped by check dams, when compared with a field survey of the accumulated sediment deposition. For the Yan River Basin, our results indicated that the designed structural parameters of check dams have evolved over the past 60 years, with higher dams (37.14% and 9.22% increase for large dams and medium dams, respectively) but smaller controlled areas (46.03% and 10.56% decrease for large dams and medium dams, respectively) in recent years. Sediment retained by check dams contributed to approximately 15.0% of the total sediment load reduction in the Yan River during 1970–2016. Thus, our developed framework can be a promising tool for evaluating check-dam effects, and this study can provide valuable information and support to decision-making for soil and water conservation and check-dam planning and management.