Silicon carbide (SiC) microlens arrays (MLAs) with a defined layout are used as an optical homogenizer in extremely high-temperature environments due to their excellent physicochemical properties. In this paper, a novel template-oriented-assembly microsphere lithography (TMSL) method is proposed to fabricate SiC MLA. Firstly, the metal micropyramid array (MPA) template was designed and fabricated by ultraprecision cutting and then converted to a polydimethylsiloxane (PDMS) surface. After that, the microspheres were assembled into a monolayer on the inverted MPA of PDMS. Subsequently, the microsphere array monolayer (MSM) was used as the stamper in the hot embossing process to create the photoresist MLA mask. Finally, the patterns on the photoresist mask were transferred to the SiC substrate by inductively coupled plasma (ICP) etching. The layout of lens units was determined by the MPA template and the positioning accuracy of MLA unit is mainly influenced by the form error in MPA mold manufacturing process. The transfer mechanism from the metal MPA template to SiC MLA was studied, and the transfer characteristics of theoretical analyses and experimental results were compared, confirming the feasibility and advantages of the TMSL method.