The invention relates to a preparation method of a carbon nano tube composite bismuth molybdate environmentally friendly and deep water treatment agent. The preparation method comprises the following steps: (1), carboxylation and amination modification are performed on a carbon nano tube and 2,4,6-trifluoro-5-chloro-pyrimidine is modified to prepare a reaction type carbon nano tube; (2), bismuth salt, a stabilizer, a template agent and the reaction type carbon nano tube are added into a phosphate buffer solution, and stirring is performed for 30 to 60 min, so as to form turbid liquid; molybdate is dissolved into the phosphate buffer solution, and then the phosphate buffer solution is added into the turbid liquid, so as to form a transparent solution; (3), the product is obtained after filtering and drying. The preparation method provided by the invention has the advantages that the cost is low, the preparation method is simple, requirements for equipment are low, and the maneuverability is excellent; the water treatment agent can be used for removing high concentration organic pollutants in water, is suitable for deep treatment on various wastewater, environmental protection and zero secondary pollution are achieved, and the water treatment agent is antibacterial, deodorant and can absorb other heavy metal ions and the like.