In this paper, we focus on joint channel estimation (JCE) of multi-cell networks, which is the basis for application of multi-cell cooperative. For overcoming the weakness that the existing multi-cell JCEs need power delay profile (PDP) knowledge of all multiple cells remained the same and known by receiver or pilot sequence sets of all cells being identical and other limitations, the paper presents a time domain correlation based JCE algorithm for multi-cell cooperative network when PDPs of multiple cells are not same and unknown and derives the corresponding Cramer-Rao bound (CRB). Then, by using Generalized Akaike Information Criterion (GAIC) to estimate PDPs of all cells for reducing the signal space of channel estimation, the paper further optimizes this JCE algorithm. Simulation results illustrate the proposed algorithms have good mean square error (MSE) performance, and corresponding space frequency block coded (SFBC) cooperative multi-cell transmission system have the good bit error rate (BER) performance too.