Abstract: Transmission-type X-ray sources exhibit significant advantages in customized radiation applications such as high-precision imaging, materials analysis, and medical diagnosis due to their superior radiation output symmetry and highly tunable characteristics. The development of transmission-type X-ray source devices based on micro-nanostructured molybdenum anode targets not only promises to achieve microfocused radiation characteristics and enhanced brightness but also enables more precise X-ray control. However, under high-power operating conditions, thermal management of the target material emerges as a critical bottleneck limiting the enhancement of X-ray radiation dose and brightness. This issue is particularly prominent in practical applications, significantly impacting device longevity and operational stability. A theoretical model for the thermal response of micro - nanostructured molybdenum anode targets was established, comprehensively incorporating heat conduction, radiation heat transfer, and electron beam energy deposition. Through systematic analysis of the relationships among electron beam energy, transmission target structural parameters, and temperature distribution, combined with multi-parameter optimization calculations, the optimal molybdenum target dimensions of 1 μm in diameter and 2.6 μm in thickness were determined, achieving an optimal balance between radiation performance and thermal stability. To further address thermal instability issues, a device thermal management strategy utilizing alternating excitation of rotating molybdenum anode targets was proposed. This strategy significantly enhances heat dissipation efficiency through an innovative rotational mechanism design. Theoretical calculations indicate that by introducing additional heat dissipation pathways, this structure can withstand electron beam bombardment with current densities up to 282.28 mA/cm², representing a 44.45-fold performance improvement compared to single micro-nanostructured molybdenum targets. These research findings provide crucial theoretical guidance and innovative insights for developing next-generation high-performance transmission-type microfocused X-ray sources, potentially advancing related technologies in high-precision applications. Furthermore, the thermal management strategy proposed in this study serves as a valuable reference for the thermal design of other high-power micro-nanodevices.