This aim of this study is to improve the guidance role of the fuel tax rate and bus departure quantity on travel mode choice. Car and bus travel are chosen as the research object, and a day-to-day evolution model of dual-mode network traffic flow (based on a stochastic user equilibrium model and the method of network tatonnement process) is established. Subsequently, a guidance optimization model of fuel tax rate and bus departure quantity is designed. This guidance optimization model is formulated to determine the comprehensive minimum value among system total travel time of car travel, system total comprehensive cost of bus travel, and the difference between the total operating cost of bus departure increment and the total amount of fuel tax levied on car travelers. Through numerical examples, the validity of this guidance optimization model is verified, and the influence of fuel tax rate and bus departure quantity on the traffic network is analyzed. The results show that a guidance optimization scheme based on fuel tax rate and bus departure quantity can help regulate the proportion of car travel and improve bus service quality.