In order to quantitatively reflect the impact of tunnel engineering on groundwater environment, a set of scientific and perfect evaluation system of negative effect of groundwater environment in tunnel engineering was constructed. According to Hydrogeological Survey of Railway Engineering (TB/10049-2014) and the related literatures, we established a hierarchy of tunnel project of groundwater environment negative effect evaluation model. By considering the uncertainty and unascertainty of the tunnel project of groundwater environment effect evaluation in the information, establishing evaluation index and the effect of groundwater environments, combining the unascertained measure model with AHP method to calculate the index weight, and calculating the multi-target weighted comprehensive measures, this study obtained the evaluation model based on the unascertained measure theory. Finally, an engineering example was used to verify the evaluation system, and the evaluation results were compared with the results of fuzzy comprehensive evaluation method to verify the reliability and applicability of the evaluation system.