The invention provides a mainboard LED testing method which comprises the following steps that: each LED on a mainboard to be tested is numbered, two LED numbers are randomly selected, corresponding LED working states are respectively set into a constant lightening state and a constant extinguishing state, the working states of other LEDs on the mainboard to be tested are set into flickering states, the LEDs on the mainboard to be tested are controlled to work, a constant lightening LED number and a constant extinguishing LED number are input according to the actual working state of the LEDs,the two input numbers are compared with the two selected LED numbers to ensure whether the numbers are same, if the numbers are respectively same in a comparative result, other two LED numbers are selected again and are tested, otherwise, the invention also provides a mainboard LED testing system, and the anamorphic situations of mainboard LED testing results can be reduced.