L-citrulline plays important roles in many physiological processes, and its application range is expanding rapidly. Corynebacterium glutamicum strains have the potential to be efficient L-citrulline producers. In this study, we performed optimization of L-citrulline biosynthesis operon in C. glutamicum ATCC13032 for L-citrulline production. Chromosomal integration of the integral argBEc gene from Escherichia coli (encoding natively insensitive N-acetylglutamate kinase), the deletion of the argR gene (encoding repressor ArgR), and the deletion of the argG gene (encoding argininosuccinate synthase) were achieved simultaneously by one-step genome modification and by obtaining the L-citrulline-producing strain. Then, plasmid-based overexpression of the optimized L-citrulline operon was carried out and the L-citrulline production was further improved. In fed-batch fermentation, the L-citrulline production and yield from glucose of the final strain reached 26.7 g/L and 0.18 g/g, respectively. These results indicate that optimization of L-citrulline operon in C. glutamicum is effective to construct the L-citrulline over-producing strain.