This study addresses a parallel machine production and transportation operations’ scheduling problem with a tight time window associated with the transfer and delivery process. The orders located at the parallel machines need to be delivered to customers by train. Each order must be processed within a limited completion time in order for the product to be matched with the optimal trip to its destination within the delivery period. A mathematical analysis method is used to reveal the impact of tight time windows on the scheduling of production and transportation operations. The order transfer redundancy time and order transfer waiting time are employed to reflect the impact scheduling of production on the transfer process. The order delivery redundancy time and order delivery waiting time are used to describe delivery operations. The goal is to maximize the coordination level of order transfer and delivery, which are reflected in the order transfer time and the order delivery time, respectively. Additionally, a simulated annealing algorithm using the column generation technique was developed to solve this problem. The results show that the use of the system coordination model in this method obviously improves the number of successful transfers and deliveries.