In diffusion based molecular communication, the intersymbol interference (ISI) is an important reason for system performance degradation, which is caused by the random movement, out-of-order arrival and indistinguishability of the moleclues. In this paper, a new metric called crossover distance is introduced to measure the distance between the received bit sequence and the probably tranmitted bit sequences. A new decoding scheme of conventional codes is proposed based on crossover distance, which can enhance the communication reliability significantly. The theoretic analysis indicates that the proposed decoding algorithm provides an approximately maximal likelihood estimation of the information bits. The numerical results show that compared with uncoded systems and some existing channel codes, the proposed convolutional codes offer good performance with same throughputs.