The city signed the deal on Tuesday with Future Forest and the All China Youth Federation to plant 72,000 trees and will invest about W50 million (US$ 49 million) in the tree-planting project.
The plan calls for members of the All China Youth Federation, which is affiliated with the Communist Party of China, to plant trees in Inner Mongolia.
NGOs will provide technical leadership and logistical support to planters, who might have problems in creating small oases to guarantee the survival of the saplings.
The 72,000 trees include poplar and desert willow, the only trees capable of growing with shallow roots.
According to some studies by Seoul University, if the tree-planting project is completed as scheduled, a green ecosystem in the desert will come into being by the end of next year, and will be capable of stopping the sand when winds blow from the West.
The Kubuqi is located some 600 kilometres west of Beijing and is seventh largest desert in the world.
Covered in forests until the late 19th century, it lost its vegetation as a result of early industrial development and overpopulation.
The region is known to be the source of 40 per cent of the yellow dust, which affects the Korean Peninsula every spring.
The South Koreans decided to launch this initiative because dusty thunderstorms have worsened over the past decade.
Sand can provoke serious respiratory problems and affects especially vulnerable groups like children, women and the elderly.
It can also clog air conditioning, an essential service for South Koreans during hot humid summers.