The invention provides an uplink channel estimation method, a pilot signal transmission method and a base station. The uplink channel estimation method comprises the steps of: configuring an uplink pilot resource for target user equipment which is positioned in a preset region; receiving pilot signals of user equipment in the preset region, and calculating uplink channel estimated values of the user equipment in the preset region separately; estimating long-term channel characteristic parameters of an uplink channel of the target user equipment based on the uplink channel estimated values of a preset number of the user equipment in the preset region; reconfiguring the uplink pilot resource of the target user equipment according to the long-term channel characteristic parameters of the uplink channel of the target user equipment; and receiving a pilot signal of the target user equipment, performing instantaneous channel estimation on the uplink channel of the target user equipment, and regarding an estimated result as an uplink channel estimated value of the target user equipment. By adopting the uplink channel estimation method, the pilot signal transmission method and the base station, the channel estimation quality can be improved.