The invention provides a MANWMB (micro nano aeration wastewater microbial bioremediation) system for black and odorous river control and a control method thereof. The MANWMB system mainly comprises a river, a first reaction area, a second reaction area, a third reaction area, a fourth reaction area, a micro nano plug-flow aerator, a microbial carrier, a microbial carrier fixing rope, a microbial carrier fixing column, a stirrer, a microorganism adding device, an online monitoring system, photovoltaic power generation equipment and the like. By establishing different reaction areas, installing filler and adding microbial strains in the river, enough dissolved oxygen is provided for the river under the action of the micro nano plug-flow aerator, and the water quality is monitored in real time through the online monitoring system to finally guarantee the purification and remediation of the black and odorous river. Compared with the existing river control technology, the system provided by the invention is compact in structure and reasonable in layout, and related technological parameters can be adjusted according to the water quality so as to guarantee up-to-standard water quality. Meanwhile, since no chemical agent is used in the whole control process, the MANWMB system is an environment-friendly and efficient novel black and odorous river remediation technology.