Road safety affects health and development worldwide; thus, it is essential to examine the factors that influence crashes and injuries. As the relationships between crashes, crash severity, and possible risk factors can vary depending on the type of collision, we attempt to develop separate prediction models for different crash types (i.e., single- versus multi-vehicle crashes and slight injury versus killed and serious injury crashes). Taking advantage of the availability of crash and traffic data disaggregated by time and space, it is possible to identify the factors that may contribute to crash risks in Hong Kong, including traffic flow, road design, and weather conditions. To remove the effects of excess zeros on prediction performance in a highly disaggregated crash prediction model, a bootstrap resampling method is applied. The results indicate that more accurate and reliable parameter estimates, with reduced standard errors, can be obtained with the use of a bootstrap resampling method. Results revealed that factors including rainfall, geometric design, traffic control, and temporal variations all determined the crash risk and crash severity. This helps to shed light on the development of remedial engineering and traffic management and control measures.