The flexible interconnection of microgrids (MGs) adopting back-to-back converters (BTBCs) has emerged as a new development trend in the field of MGs. This approach enables larger-scale integration and higher utilization of distributed renewable energy sources (RESs). However,their stability characteristics are very different from single MG due to the control characteristics of flexible interconnection. Meanwhile, the uncertainty and stochastic dependence structures of RESs and loads create challenges for stability analysis and cooperative control. In this paper, a probabilistic small-signal stability assessment and cooperative control framework is proposed for interconnected MGs via BTBCs. First, a cooperative control architecture for MGs is constructed. Then, a small-signal model of interconnected MGs via BTBCs containing primary control and secondary control is developed. This model facilitates the analysis of the impacts of BTBCs and various control strategies on the system stability. Subsequently, Copula functions and polynomial chaos expansion (PCE) are combined to achieve the probabilistic small-signal stability assessment. On this basis, the parameters of the cooperative control are optimized, enhancing the robustness of interconnected MGs via BTBCs. Finally, a case of interconnected MGs via BTBCs are built in MATLAB/Simulink to verify the accuracy and effectiveness of the proposed framework.