Understanding crash causation to the extent needed for applying countermeasures has always been a focus as well as a difficulty in the field of traffic safety. Previous research has been limited by insufficient crash data and analysis methods more suitable to single crashes. The use of crashes and near crashes (CNCs) and naturalistic driving studies can help solve the data problem, and use of pre-crash scenarios can identify the high-prevalence causes across multiple crashes of a given scenario. This study therefore proposes a two-stage crash causation analysis method based on pre-crash scenarios and a crash causation derivation framework that systematically categorizes and analyzes contributing factors. From the Shanghai Naturalistic Driving Study (SH-NDS), 536 CNCs were extracted, and were grouped into 23 different pre-crash scenarios based on the National Highway Traffic Safety Administration (NHTSA) pre-crash scenario typology. In-depth investigations were conducted, and CNCs sharing the same scenario were analyzed using the proposed framework, which identifies causation patterns based on the interaction of the framework’s road user, vehicle, roadway infrastructure, and roadway environment subsystems. Through statistical analysis, the causation patterns and their contributing factors were compared for three common pre-crash scenarios of highest incidence: rear-end, lane change, and vehicle-pedalcyclist. Braking error in low-speed car following, following too closely, and non-driving-related distraction were important causes of rear-end scenarios. In lane change scenarios, the main causation patterns included illegal use of turn signals and dangerous lane changes as critical factors. Pedalcyclist scenarios were particularly impacted by visual obstructions, inadequate lanes for non-motorized vehicles, and pedalcyclists violating traffic regulations. Based on the identified causation patterns and their contributing factors, countermeasures for the three common scenarios are suggested, which provide support for safety improvement projects and the development of advanced driver assistance systems.