Functional magnetic resonance imaging (fMRI) combined with optogenetic neural manipulation provides a powerful framework for mapping brain-wide effective connectivity (EC). In this study, we developed a high-throughput approach integrating spatiotemporally programmable optogenetic stimulation with fMRI, enabling precise and flexible neural manipulation across the mouse cortex. Using a digital micromirror device (DMD) coupled with an optical fiber bundle inside an MR scanner, we delivered patterned photostimulation while acquiring fMRI data. By sequentially stimulating nine atlas-defined cortical regions within a single fMRI run, we achieved high-throughput mapping of cortical EC. This approach also offers versatility in experimental design, such as functional localizer-based stimulation planning or viral tracing-based circuit-specific targeting, facilitating a more refined investigation of functional networks. The integration of mouse fMRI with flexible stimulation paradigms provides a precise method for studying large-scale neural interactions, paving the way for high-throughput exploration of circuit-level mechanisms underlying cognition and behavior.