Multi-walled carbon nanotubes were synthesized on Ni catalyst using thermal chemical vapor deposition. By introducing ammonia gas during the CNT synthesis process, clean and vertically aligned CNTs without impurities could be prepared. As the ammonia gas increased a partial pressure of hydrogen in the mixed gas during the CNT synthesis process, we could control the CNT synthesis rate appropriately. As the ammonia gas has an etching ability, amorphous carbon species covering the catalyst particles were effectively removed. Therefore catalyst particles could maintain their catalytic state actively during the synthesis process. Finally, we could obtain clean and vertically aligned CNTs by introducing $NH_3$ gas during the CNT synthesis process.