BIM-based rule checking systems are helpful for identifying potential concerns and flaws during the building design process. Currently, there is a lack of useful user interfaces for flexible rule manipulations and better tractability of the design intentions when rule violations occurred. This study aims to develop a BIM-based rule checking interface for users to address: (1) the current inflexible laborious coding process of rules, and (2) the low capability to describe rule influence comprehensively on the model designs. A research question is raised that whether the design adjustments against rule violations, such as making BIM elements changed, can be further traced their influence by an interface to prevent derived violations. A two-layered logic-based rule evaluation interface is developed to establish the rules aimed at meeting users' needs, and to identify design dependency topologically related to the involved BIM elements. A case study with a partial 7-story building section is used to evaluate the interface, and results show that the dependency between rule violations and their affected BIM elements can be successfully retrieved. It helps users to make the adjustment and identify influences of design changes to avoid further derived rule violations. A future direction of the study is capability evaluations for typical building engineers and architects to translate their design intentions and local rules by using the proposed interface with real building projects.