This paper is focused on analyzing the risk distribution characteristics in short weaving areas of urban interchanges. The study was carried out on merge-diverge weaving areas with different lengths of 350 m, 450 m, and 550 m. To evaluate and identify the risk, the average speed, speed standard deviation, acceleration range, and average absolute value of acceleration were selected as indicators. Vissim simulation was applied to collect the identification indicator value of 21 typical lane sections. The results show that the risk is concentrated at the 3/4 section and exit section of the outer lane. The vehicle-operating status of the inner and middle lanes is almost unaffected. The operating speed of the outer lane is approximately 4/5 of the same position in the inner lane at 3/4 of the length of the weaving segment, while the speed standard deviation is approximately 2 times greater, and the acceleration range is approximately 2–3 times greater. Moreover, the acceleration of the average absolute value is also approximately 2–3 times greater. To balance the risk distribution, an optimization method is proposed based on the result analysis. Compared with the original design, the results show that a reasonable method of traffic organization for the complex weaving area can effectively improve the risk distribution in the weaving area and reduce the high peak of risk concentration. These results provide a basis for the optimization method and traffic organization of short weaving areas of municipal interchanges.