Homologous recombination is an important technique that is used to modify mammalian genome. Here, we constructed an efficient common gene targeting vector based on the plasmid pBS246. The vector consisted two positive selection markers, neomycin resistance gene (neo) and enhanced green fluorescent protein gene (EGFP) flanked by locus of X-over P1 (LoxP) sites. Two synthesized multiple cloning sequences MCS-1 and MCS-2 that contain several “8 bp cutter” enzyme sites were placed in outside of LoxP sites. Additionally, a negative selection marker HSV-tk (herpes simplex virus thymidine kinase) gene was located adjacent to MCS-1 site. The constructed vector was named pGT-V1, and its functions were characterized in C2C12 cells. The vector had the following unique features: 1) EGFP was used to monitor instantly the transfection rate that was essential for increasing the efficiency of gene knockout (KO); 2) The EGFP marker located between two LoxP sites was able to be removed from KO positive cells to avoid the potential damage of selection markers to the recipient cells. The process could be monitored visually and the positive cells without selecting markers (the loss of green fluorescent cells) could be sorted out by either flow cytometry or immunomagnetic beads; 3) “8 bp cutter” restriction sites were embedded in MCS sequences, which then enhanced the versatility of this vector. In summary, the constructed plasmid optimized the vector of gene targeting and provided a new technique means for the transgenic animal research.