The invention belongs to the technical field of tertiary oil recovery, and particularly relates to a method for increasing single-well output of a heavy oil well through an indigenous microorganism. The method comprises the following steps that the indigenous microorganism of a testing oil well is detected; the testing oil well is screened; an activator of the testing oil well is screened; the injecting amount of the activator is determined; the field injecting technology of the activator is determined; and the field test of the testing oil well is conducted. According to the method for increasing the single-well output of the heavy oil well through the indigenous microorganism, the investment cost is low, the implementation technology is simple, and the situations of well sanding and casing pipe damage do not occur; the viscosity of heavy oil can be greatly reduced, the flowing property of crude oil is improved, oil-water interfacial tension can be effectively reduced, the oil-water mobility ratio is reduced, the period of validity is long and exceeds 20 months, the oil enhancement effect is good, the range of daily oil increment of a single well is more than 50%, and the input-output ratio is greater than 1:3; and therefore, the method for increasing the single-well output of the heavy oil well through the indigenous microorganism is an economical and effective method to improve the output of the heavy oil well and can be widely applied to a single well huff and puff oil production technology of the heavy oil well.