A method of performing uplink channel estimation and a base station using the same are provided. The method is applicable to serve at least two UE equipments (UEs) in a communication system. The at least two UEs are located in at least two beam sectors respectively. The base station comprises a plurality of antennas. The method includes: determining whether multipath of the at least two UEs passing through a same beam sector; assigning a first and a second training sequence for a first UE and a second UE of the at least two UEs respectively; receiving a reference signal, wherein the reference signal is transmitted by the first UE and the second UE according to the first and the second training sequence; and performing channel estimation for the first UE and the second UE according to the reference signal, the first and the second training sequence.