This study aims at identifying crash-influencing factors by facility type of Nagoya Urban Expressway, considering the interaction of geometry, traffic flow, and ambient conditions. Crash rate (CR) model is firstly developed separately at four facility types: basic, merge, and diverge segments and sharp curve. Traffic flows are thereby categorized, and based on the traffic categories, the significances of factors affecting crashes are analyzed by principal component analysis. The results reveal that, the CR at merge segment is significantly higher than those at basic and diverge segments in uncongested flow, while the value is not significantly different at the three facility types in congested flow. In both un- and congested flows, sharp curve has the worst safety performance in view of its highest CR. Regarding influencing factors, geometric design and traffic flow are most significant in un- and congested flows, respectively. As mainline flow increases, the effect of merging ratio affecting crash is on the rise at basic and merge segments as opposed to the decreasing significance of diverging ratio at diverge segment. Meanwhile, longer acceleration and deceleration lanes are adverse to safety in uncongested flow, while shorter acceleration and deceleration lanes are adverse in congested flow. Due to its special geometric design, crashes at sharp curve are highly associated with the large centrifugal force and heavy restricted visibility.