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Three-way decision, an outstanding method to handle decision-making uncertainties, relies on essentially the loss functions derived from the Bayesian risk decision process. Actually, there are plentiful loss functions that depend on the subjective judgment of decision-makers under different decision scenarios, lacking uniform and objective measurement frameworks. This study pays attention to the real clinical diagnosis, and constructs a weighted probability kernel multi-granularity three-way decision method (WKMG-TWD) integrating gray relation analysis (GRA) over a multi-source heterogeneous decision information system (MHDIS). The method establishes a standardized data-driven calculation framework of loss functions. Foremost, the multi-kernel probabilistic similarity is defined and granularity's weights with knowledge consistency are explored. Subsequently, a weighted probability kernel multi-granularity rough set (WKMGRS) is constructed in this paper. Secondly, to introduce the three-way decision, this study proposes the cost-sensitive individual loss functions considering the correlation determined by GRA between decision objects and different decision classes. Ultimately, this study establishes and applies a three-way iterative classification model to hypertension diagnosis. The experimental results confirm the effectiveness and superiority of the model. The main contribution of this paper is twofold. One is to offer a uniform calculation framework for loss functions and granularity's weights. The other is to furnish invaluable guidance for solving complex medical decision-making problems. [ABSTRACT FROM AUTHOR]