Freeway bottleneck areas are prone to congestion and have high accident risk. A variable speed limit provides technical support for alleviating congestion and improving traffic safety in such areas. The existing variable speed limit rules in the related literature have a single focus, and most of them do not give specific quantitative speed limits. In this study, a variable speed limit system suitable for freeway bottleneck areas was constructed. Variable speed limit rules under different levels of traffic congestion and adverse weather conditions were designed, and the parameters for freeways were defined. Then, the VISSIM microscopic traffic simulation software was used to build two bottleneck scenarios of a tunnel area and a merging area for simulation tests. The research shows that in these two scenarios, reasonable speed limits can effectively reduce roadway delays and improve the operational efficiency of bottleneck areas in certain traffic flow ranges (e.g., a medium flow of around 900 pcu/h/lane). Unreasonable speed limits in low flow inhibit freeway efficiency more significantly. When congestion has already formed with high flow, different speed limits have a limited effect on efficiency improvement. The research results reported in this paper can provide a theoretical reference for the design and practical application of variable speed limit systems in freeway bottleneck areas. This provides a certain contribution to sustainable traffic development.