Abstract Filler-reinforced polymer composites demonstrate pervasive applications due to their strengthened performances, multi-degree tunability, and ease of manufacturing. In thermal management field, polymer composites reinforced with thermally conductive fillers are widely adopted as thermal interface materials (TIMs). However, the 3D-stacked heterogenous integration of electronic devices have posed the problem that high-density heat sources are spatially distributed in the package. This situation puts forward new requirements for TIMs, where efficient heat dissipation channels must be established according to the specific distribution of discrete heat sources. To deal with this challenge, a 3D printing-assisted streamline orientation (3D-PSO) method was proposed to fabricate composite thermal materials with 3D programmable microstructures and orientations of fillers, which combines the shape-design capability of 3D printing and oriented control ability of fluid. The mechanism of fluid-based filler orientation control along streamlines were revealed by mechanical analysis of fillers in matrix. Thanks to the designed heat dissipation channels, composites showed better thermal and mechanical property in comparison to random composites. Specifically, the thermal conductivity of 3D mesh-shape PDMS/LM composite was 5.8 times that of random PDMS/LM composite under filler loading of 34.8 vol%. The thermal conductivity enhancement efficiency of 3D mesh-shape PDMS/CFs composite reached 101.05% under filler loading of 5.2 vol%. In the heat dissipation simulation of 3D-stacked chips, the highest temperature with 3D-PSO composite was 42.14 ℃ lower than that with random composites. This is mainly attributed to the locally aggregated and oriented fillers structure in fluid channels which contributes to thermal percolation phenomena. The 3D-PSO method exhibits excellent programmable design capability to adopt versatile distributions of heat sources, paving a new way to solve the complicated heat dissipation issue in 3D-stacked chips integration application.