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Global food demand will increase over the next few decades, and sustainable agricultural intensification on current cropland may be a preferred option to meet this demand. Mapping cropping intensity with remote sensing data is of great importance for agricultural production, food security, and agricultural sustainability in the context of global climate change. However, there are some challenges in large-scale cropping intensity mapping. First, existing indicators are too coarse, and fine indicators for measuring cropping intensity are lacking. Second, the regional, intra-class variations detected in time-series remote sensing data across vast areas represent environment-related clusters for each cropping intensity level. However, few existing studies have taken into account the intra-class variations caused by varied crop patterns, crop phenology, and geographical differentiation. In this research, we first presented a new definition, a normalized cropping intensity index (CII), to quantify cropping intensity precisely. We then proposed a Bayesian network model fusing prior knowledge (BNPK) to address the issue of intra-class variations when mapping CII over large areas. This method can fuse regional differentiation factors as prior knowledge into the model to reduce the uncertainty. Experiments on five sample areas covering the main grain-producing areas of mainland China proved the effectiveness of the model. Our research proposes the framework of obtain a CII map with both a finer spatial resolution and a fine temporal resolution at a national scale.