A network-based positioning mechanism is proposed. A serving BS first allocates radio resource to a target UE for network-based positioning in a wireless communication system. The target UE then transmits a positioning reference signal (PRS) to the serving BS and a plurality of cooperative BSs at the same time instant. All the cooperative BSs then conduct PRS detection and TOA measurements. Finally, the serving BS conducts positioning estimation based on the TOA measurement results. In one novel aspect, only one PRS transmission is required in one positioning opportunity for one positioning result. Candidates of PRS are selected with respect to different scenarios and allocated in a PRS resource region. Multiple positioning opportunities and multiple reference signals may be multiplexed over time, frequency or code domain in the PRS resource region. In one embodiment, the PRS is configured in such a way that both radio resource consumption and interference is minimized.