In response to the international trend of educational decentralization in recent decades, many elementary and junior high schools in Taiwan had adopted sub-budgets of the "subordinate unit budgets" in the Local Education Development Fund for years so as to develop school-based budgeting. Furthermore, with the decline in birth rates and the need of enrollment, the establishment of specialist schools has been encouraged nationwide in Taiwan since 2007. These specialist schools took advantage of specific geographical and cultural features to develop their localized educational features so that their educational competitiveness and qualities could be enhanced. The major purpose of this paper is to examine the relationships among school-based budgeting, innovative management, and school effectiveness in Taiwan's specialist schools. This paper adopts a questionnaire and employs structural equation modeling for the purpose of analysis. Innovation is a determining point whether schools can make progress or not. The results of the study show that innovative management conduces to direct enhancement of school effectiveness. Moreover, innovative management will be carried out more smoothly when school-based budgeting is performed positively. However, it was surprising to find that school-based budgeting cannot enhance the school effectiveness directly. Instead, it can promote the improvement of school effectiveness indirectly through innovative management.