The seeding mechanism of equatorial plasma bubbles (EPBs) in the ionosphere has not been fully understood for several decades. Before investigating the complex seeding process by atmospheric gravity waves, which have been considered as a possible candidate, we investigate the vertical neutral wind effect on the EPB seeding by making the numerical simulation setup as simple as possible. It is presented that the vertical wind over the dip equator with an amplitude of as low as 5 m/s can seed EPBs effectively. The upward wind reduces the eastward current and produces the eastward polarization electric field, so that the bottomside F region pushed by the upward wind is going to form upwellings and penetrate into the topside F region accelerated by the Rayleigh‐Taylor instability. It is suggested that the vertical wind perturbations driven by gravity waves should play an important role in seeding EPBs.