In this research, a new data mining-based design approach has been developed for designing complex mechanical systems such as a crashworthy passenger car with uncertainty modeling. The method allows exploring the big crash simulation dataset to design the vehicle at multi-levels in a top-down manner (main energy absorbing system, components, and geometric features) and derive design rules based on the whole vehicle body safety requirements to make decisions towards the component and sub-component level design. Full vehicle and component simulation datasets are mined to build decision trees, where the interrelationship among parameters can be revealed and the design rules are derived to produce designs with good performance. This method has been extended by accounting for the uncertainty in the design variables. A new decision tree algorithm for uncertain data (DTUD) is developed to produce the desired designs and evaluate the design performance variations due to the uncertainty in design variables. The framework of this method is implemented by combining the design of experiments (DOE) and crash finite element analysis (FEA) and then demonstrated by designing a passenger car subject to front impact. The results show that the new methodology could achieve the design objectives efficiently and effectively. By applying the new method, the reliability of the final designs is also increased greatly. This approach has the potential to be applied as a general design methodology for a wide range of complex structures and mechanical systems.