Rural hybrid renewable energy systems represent an effective means to promote rural energy transition. This paper proposes a two-stage dynamic planning strategy that aims to develop site-specific planning strategies and fair market mechanisms to maintain and stimulate the sustainability. The first stage establishes a multidimensional sustainability evaluation system for rural hybrid renewable energy systems, dynamically selecting optimal renewable resource solutions for various regions through multi-criteria decision making. The results of the first stage are inputted into the second stage, which configures the optimal capacity with the goal of optimal integrated performance under a laddered dynamic carbon-green certificate coupling trading mechanism that considers new energy life-cycle carbon emissions and carbon emission reduction attribute of green certificates, while also factoring in green certificate and carbon emission right conversions during the operational phase. Taking five helping counties in China as experimental cases, the analysis of the simulation results in the first stage shows that all the multidimensional evaluation indicators are the main factors affecting the sustainability. In the second stage, the adoption of the carbon-green certificate coupling system successfully avoided cross-subsidies totaling 1.42x107 CNY and an overlooked carbon emission of 6.22x107 kg, thereby enhancing emission reduction effectiveness and fairness in the trading mechanism. Furthermore, the conversion of carbon emission rights and green certificates yielded additional revenue, further bolstering sustainability. Consequently, this planning strategy effectively facilitated the sustainable adoption of rural hybrid renewable energy systems by users, while also providing a viable planning solution for rural energy development.