Controllable orientation architecture possesses tunable thermal behavior for effective heat dissipation in unidirectional product fields, meanwhile without interference with adjacent components. Herein, we proposed a variable orientation strategy in material extrusion of short carbon fiber (SCF) reinforced polymer composites framework with spatially tunable thermal properties. It was achieved due to the following reasons: (Ⅰ) Inherent shear flow in the nozzle; (Ⅱ) Increasing tensile flow by changing the ratio between the printing speed of monofilament and the feeding speed of filament (Vp/f); (Ⅲ) Further surface tension due to thinning monofilament by varying Vp/f. The SCF with different orientations and content reinforced polyether-ether-ketone (PEEK) composites were successfully fabricated. The microcosmic orientation of SCF could be programmed from a three-layer hierarchical framework to a single-layer oriented framework at different Vp/f. Benefit from variable orientation, the through-plane thermal conductivity of SCF/PEEK composites achieved a thermal conductivity enhancement of 173.9 %. In addition, the simulated application of SCF/PEEK composites in the CPU of the computer showed excellent heat transfer during heating. Further, the thermal conductivity mechanism of the synergistic influence between Vp/f and SCF content was analyzed by cross-sectional microstructure. The proposed strategy in this work for fabricating variable orientation of SCF reinforced polymer composites showcases great application prospects in electronic devices and unidirectional product fields.