Taiwan has noticed relative disadvantages in rural areas and offered more scholarship opportunities for aboriginal and low-income students. Moreover, the Educational Priority Area program was implemented in 1996 to invest additional funds in rural schools. Although the average mathematics ability of Taiwanese students ranks high in the Programme for International Student Assessment (PISA), the cost-benefit outcome of government funding in rural areas is inadequate. This paper, therefore, tries to explain low student achievement in rural areas with the multilevel modeling (HLM). Data were gathered from 5,581 Taiwanese students in 236 junior high schools using stratified random sampling. Of the data, 2,358 students from 112 rural area schools and 3,223 students from 124 non-rural area schools were sampled. The results demonstrate the importance of distinguishing between resources and investments, and shifts focus from comparisons of the influence of families and schools preexisting conditions to discussions of improvement strategies on mathematics performance. Both families and schools are limited by their resources, but the findings presented in this study suggest that families and schools can improve student achievement with appropriate investments.