The information of trip demand as the freight origin-destination (O-D) matrices plays a significant role in intercity transportation engineering and planning. Access to this matrix from conventional methods needs to spend time, money and human resources. During the recent years, numerous studies have been conducted in order to obtain the freight O-D matrix using freight vehicle count information in network links. Furthermore, the estimation of O-D matrix and its communicating with freight vehicles can greatly help planners improve logistic, safety and the maintenance issues. This paper presents a method based on the minimization of the deviations between the observed and estimated values for finding the freight O-D matrix. To solve the model, traffic count data of trucks in the network links as well as other related information resources are used. The model is solved for a case study in Iran using meta-heuristic Simulated Annealing Algorithm.