The weaving area is an important junction that affects the efficiency and traffic safety at the municipal interchanges. To explore the factors affecting traffic efficiency and the spatial distribution characteristics of traffic risks in the weaving areas of municipal interchanges, this study employed a microscopic traffic software of Vissim to construct a simulation model of weaving areas and evaluate the impact of road and traffic design parameters in the short weaving on traffic efficiency and risks, which includes ramp delay, mainline through lane (TL) traffic delay, average ramp speed, TL average speed, and collision rate. Through variance analysis via a large number of simulation scenarios, the weaving length is identified as the most important factor affecting traffic efficiency and risks in the short weaving area. Subsequently, three different types of weaving lengths with 350 m, 450 m, and 550 m were set to conduct the sensitivity analysis based on four performance indexes of mean acceleration and deceleration, acceleration range, deceleration range, and speed standard deviation as the representative variables of spatial risk distribution. The simulation results illustrate that a shorter weaving length has a significant influence on risk distribution, especially the highest risk probability at the positions after three-quarters of the inner and outer lanes in the short weaving area at the municipal interchange. Finally, this study verified the traffic risk reduction method of having traffic safety facilities and traffic organization at the complex interchange with double-entry and single-exit weaving areas in the city of Guangzhou, China. The research proposed a method to analyze the influence of the design parameters in the short weaving area on traffic efficiency and safety and provided a reference for the risk spatial distribution analysis and improvement in the short weaving area.