Users increasingly interact with content across multiple domains, resulting in sequential behaviors marked by frequent and complex transitions. While Cross-Domain Sequential Recommendation (CDSR) models two-domain interactions, Multi-Domain Sequential Recommendation (MDSR) introduces significantly more domain transitions, compounded by challenges such as domain heterogeneity and imbalance. Existing approaches often overlook the intricacies of domain transitions, tend to overfit to dense domains while underfitting sparse ones, and struggle to scale effectively as the number of domains increases. We propose \textit{GMFlowRec}, an efficient generative framework for MDSR that models domain-aware transition trajectories via Gaussian Mixture Flow Matching. GMFlowRec integrates: (1) a unified dual-masked Transformer to disentangle domain-invariant and domain-specific intents, (2) a Gaussian Mixture flow field to capture diverse behavioral patterns, and (3) a domain-aligned prior to support frequent and sparse transitions. Extensive experiments on JD and Amazon datasets demonstrate that GMFlowRec achieves state-of-the-art performance with up to 44\% improvement in NDCG@5, while maintaining high efficiency via a single unified backbone, making it scalable for real-world multi-domain sequential recommendation.