The invention belongs to the technical field of sea water desalination and water treatment, and relates to a cleaning method of an ultrafiltration membrane in sea water desalination by the whole membrane technology. The cleaning method comprises the following steps of: transporting pre-treated sea water to a raw water inlet of an ultrafiltration device; mixing with ultrafiltration circulating concentrated water transported by an ultrafiltration circulating pump, wherein the mixture enters into the ultrafiltration device to be filtered to obtain ultrafiltration water entering into a closed ultrafiltration water buffer tank; then, transporting the ultrafiltration water by a low pressure pump, wherein one part of the water flowing through a security filter is pressurized by a high pressure pump and enters into a nanofiltration/reverse osmosis device through a check valve, while the residual water enters into an energy recovering device and exchanges energy with concentrated water of the nanofiltration/reverse osmosis device, then is transported to the nanofiltration/reverse osmosis device through the pressurizing pump to prepare nanofiltration/reverse osmosis water; feeding nanofiltration/reverse osmosis water after energy exchange into an ultrafiltration cleaning water tank, and discharging residual concentrated water through an overflow opening on the upper part of the ultrafiltration cleaning water tank. The cleaning method is reliable in process, simple and convenient to operate, lower in energy consumption, good in economic and social benefits and environment-friendly.