The invention discloses a tri-cistron muscle specific two-way co-expression gene transferant and a preparation method thereof. The gene transferant comprises an MARs cow matrix attachment region, short hairpin RNA (shRNA) taking the third exon (926-947 loca) of cow muscle colyone as a target spot, an optimally synthesized muscle specific promoter (MRF4), a humanization n-3 desaturase gene (FAD3), an internal ribosome entry site (IRES), a red fluorescent protein gene (DsRed) and a termination signal region (SV40polyA), and the independent gene transferant does not have a pronucleus main vector sequence. According to the tri-cistron muscle specific two-way co-expression gene transferant and the preparation method, an RNA interference technology is firstly combined with the muscle specific overexpression FAD3 and DsRed, therefore, gene knock-down and inverse overexpression of related genes can be performed simultaneously, and a novel thought and approach can be supplied for safely and efficiently improving characters, such as muscle and disease related characters, controlled by polygenes.