In the era of the knowledge economy, understanding how job skills influence salary is crucial for promoting recruitment with competitive salary systems and aligned salary expectations. Despite efforts on salary prediction based on job positions and talent demographics, there still lacks methods to effectively discern the set-structured skills' intricate composition effect on job salary. While recent advances in neural networks have significantly improved accurate set-based quantitative modeling, their lack of explainability hinders obtaining insights into the skills' composition effects. Indeed, model explanation for set data is challenging due to the combinatorial nature, rich semantics, and unique format. To this end, in this paper, we propose a novel intrinsically explainable set-based neural prototyping approach, namely \textbf{LGDESetNet}, for explainable salary prediction that can reveal disentangled skill sets that impact salary from both local and global perspectives. Specifically, we propose a skill graph-enhanced disentangled discrete subset selection layer to identify multi-faceted influential input subsets with varied semantics. Furthermore, we propose a set-oriented prototype learning method to extract globally influential prototypical sets. The resulting output is transparently derived from the semantic interplay between these input subsets and global prototypes. Extensive experiments on four real-world datasets demonstrate that our method achieves superior performance than state-of-the-art baselines in salary prediction while providing explainable insights into salary-influencing patterns.