Microchannel cooling technology using nanofluid is one of the effective ways to solve the rapid heat dissipation in a limited space for high power density device. In this work, the field synergy and heat transfer performance of nanofluid in the microchannel with non-uniform internal spoiler cavities configuration based on conjugate heat transfer and homogenous model were investigated. The heat transfer enhancement mechanism of nanofluid in this complex microchannel was discussed through the analysis of field synergy angle, field synergy factor, and flow and heat transfer characteristics. It was found that the flow and heat transfer performance of the nanofluid in the microchannel can be well explained by the field synergy principle. The nanofluid heat transfer enhancement phenomenon could be attributed to the improvement of the field synergy of the thermal boundary layer under the axial thermal conductive effect. In addition, the field synergy analysis of nanofluid in complex microchannel revealed that the heat transfer enhancement was affected by the combination of perturbation effect, the axial thermal conduction effect and the thermal boundary redevelopment.