A method, a base station and a user equipment for transmitting physical resource blocks and estimating channels are provided. The method includes: scheduling, by a base station, M PRBs for the user equipment, and configuring reference signal patterns for the M PRBs as following: allocating (X−1)M+1 demodulation reference signal subcarriers for M PRBs in a frequency domain, configuring only one demodulation reference signal subcarrier within a range of (−N, N] subcarriers in a border of every two PRBs, where locations of the rest (X−2)M+2 demodulation reference signal subcarriers keep consistent with locations of demodulation reference signal subcarriers in M contiguous first demodulation reference signal patterns in a frequency domain; and transmitting the configured M PRBs to the user equipment, so that the user equipment performs joint channel estimation according to the configured M PRBs. This saves reference signal overheads and optimizes data transmission rate.