Laser surface structuring has been demonstrated to be a versatile technology to create various functional materials by modifying solid surface properties. An interesting experimental phenomenon of self‐organized periodic microholes array formation is demonstrated by exposing an aluminum surface to femtosecond laser irradiation. The microholes with a diameter much smaller than focal laser spot size are produced along laser scan paths due to the incubation effect of multiple laser scans, and they spontaneously form a highly ordered microholes array after 80 scans. It is found that the microhole period and diameter are highly dependent on laser fluence, and controllable microholes arrays with different periods and diameters are achieved by adjusting laser fluence. The physical mechanism behind the formation of the microholes array is attributed to femtosecond laser‐induced melting and Marangoni effect. The research provides a novel processing approach to achieve controllable microholes surface materials fabrication at a high speed on metal substrates, which are of great interests for various technological applications. Self‐organized periodic microholes array formation on aluminum surface is observed via multiple femtosecond laser scans. The microholes period and diameter are found to be highly dependent on laser fluence, and controllable microholes arrays with a period from 10.5 to 33.5 µm and diameter from 5.6 to 17.4 µm are demonstrated by adjusting laser fluence.