This paper presents a model of scheduling of multi unit construction project based on an NP-hard permutation flow shop problem, in which the considered criterion is the sum of the costs of the works' execution of the project considering the time of the project as a constraint. It is also assumed that each job in the units constituting the project may be realized in up to three different ways with specific time and cost of execution. The optimization task relies on solving the problem with two different decision variables: the order of execution of units (permutation) and a set of ways to carry out the works in units. The task presented in the paper is performed with the use of a created algorithm which searches the space of solutions in which metaheuristic simulated annealing algorithm is used. The paper presents a calculation example showing the applicability of the model in the optimization of sub-contractors' work in the construction project.