Color and spatial layout are important factors that affect users’ icon cognition and play a huge role in the visual search process of icons. Guided by the user’s interactive needs, this paper aims to improve the visual search efficiency of mobile map navigation icons. The mixed design within and between subjects is adopted through the combination of theoretical and experimental research, and the subjective questionnaire method is used to explore the research. This paper explores the visual search problem of mobile map navigation icons based on color coding and layout coding. The experimental results mainly include reaction time, accuracy rate, user experience, and statistical and variance analysis. The results show that the layout of the mobile map navigation icons significantly impacts the user’s visual search. The navigation icons that use color for layout coding have the highest visual search efficiency and better user experience. Among the icons, the layout with regular color distribution and a larger area of the same color has the highest visual search efficiency for users and the best user experience; the visual search efficiency of navigation icons using color for layout coding is significantly higher than that of mobile map navigation icons.