Atmospheric pollution gradually become a focus of concern all over the world owing to its detrimental influence on human health as well as long range impact on global ecosystem. This paper investigated the relationship among SO2 emissions, GDP, fossil fuel energy consumption, energy consumption intensity, and economic structure of five provinces in China with the highest SO2 emissions spanning from 2002–2015 based on panel data model. Through comparatively analyzing the coefficients in the established panel data model for Hebei, Henan, Inner Mongolia, Shandong, and Shanxi, we can obtain that: (1) fossil fuel energy consumption made the most devotion to SO2 discharge compared with GDP, energy consumption intensity, and economic structure. And the more the fossil fuel energy consumption, the more the devotion made by it to SO2 discharge. (2) GDP devoted less to SO2 emissions than fossil fuel energy consumption, and the larger the scale of the economy, the greater the contribution made by it to SO2 emissions. (3) The higher the proportion of the secondary industry added value accounted in GDP, the more the devotion made by the economic structure and energy consumption intensity to SO2 emissions. Through analyzing the Granger causality examination results, it can be concluded that: (1) there existed a bi-directional causal relationship between fossil fuel energy consumption and SO2 emissions among five selected provinces. (2) There existed uni-directional causal nexus running from GDP to SO2 emissions, from energy consumption intensity to SO2 emissions, and from economic structure to SO2 emissions among five chosen provinces. Based on the empirical analysis, several policy implications were proposed to provide references for policy makers, which were (1) Giving full play to the guiding role of price signals, and improving the price policy for desulfurization. (2) Formulating a new comprehensive evaluation system to measure the regional development level considering economic development and environmental impacts. (3) Exploring renewable and sustainable energy sources to substitute for fossil fuel energy according to regional resources endowment. (4) Developing high value added and low pollution emissions industries and reducing the proportion of secondary industry.