The electro-fused magnesia furnace (EFMF) has complex characteristics, such as strong nonlinearity and multimodes. In this paper, the between-mode process modeling and monitoring method of the EFMF is proposed. In the original methods, the data are handled in a single mode matrices, the influence from one mode to another tends to be ignored. However, the hidden effect could be useful in process analysis and control. New method is proposed for between-mode part to establish an integrated monitoring system, which would simplify the monitoring model structure and enhance its robustness. The manifold is learned to extract the common part of between-mode transition and the monitoring performance of the between-mode is significantly improved. From the between-mode viewpoint, the multimodes processes behaviors are separated into two subspaces. In the common subspace, the underlying process-relevant variation stays invariable, showing the common contribution to multimodes processes. The specific subspace changes with the alternation of modes and has the different influences on multimodes processes modeling and monitoring. Based on subspace separation, process information is captured across modes and between-mode transition regions are distinguished from two modes. Two modes and between-mode transition models are developed respectively for multimodes processes monitoring. Experiment results show effectiveness of the proposed method.