It has been five years since the Ministry of Education in Taiwan gave an impetus to the subsidization project of reusing unused buildings and developing specialist schools in elementary/junior high schools in 2007. This study has the following aims: first, to examine the current situations of the “school innovative management” and “school effectiveness” in the specialist schools; and second, to investigate how “school effectiveness” has been enhanced in the specialist schools which implement the “school innovative management.” The questionnaire survey and the structural equation modeling (SEM) were adopted to collect and analyze data. The findings are as follows: 1. The current situations indicated that both “school innovative management” and “school effectiveness” in the specialist schools were very high; 2. after the specialist schools implemented the “school innovative management,” their school effectiveness was found to be significantly enhanced; and 3. since the “environmental innovation” had the biggest indirect effect on “school effectiveness,” the policy made by the Ministry of Education that school environment was the top priority in the specialist schools project was on the right track. Based on the above findings, this paper proposed some research suggestions.