The invention belongs to the technical field of microbe oil extraction and relates to a screening method of an indigenous microbe activator with a profile control function. The screening method comprises the following steps of 1, screening an indigenous activator carbon source according to specific oil reservoir, 2, carrying out activator phosphor source and nitrogen source screening, activator injection capability evaluation, activator concentration and injection amount optimization, and activator oil displacement effect evaluation, and screening an activator, and 3, carrying out on-site test and effect tracking according to the screened activator. The screening method has strong pertinency and is suitable for water-flooding development of heterogeneous reservoir. The screened activator has a low cost, is environmentally friendly and has no follow-up water treatment problems. The screening method has good on-site test effects and improves an extraction ratio by more than 10%. Therefore, the screening method can be widely used in the on-site test of improving an extraction ratio of reservoir water-flooding development.