The reliability optimization has achieved great concern in recent years. Nowadays, many researchers obtain allocation results which can maximize the system reliability subject to the system budget. In these researches, the effect of system’s functions is always neglected or only considering the single main function of system. In addition, there are also no obvious evidences in results to distinguish the importance level of different units. However, complex systems tend to perform multiple functions. What’s more, the use frequency of each function and the combinations of units to realize different functions are not the same. In addition, the use demand of different functions is decided by different task environments, the demand differentiation of functions has led to the usage of frequency of various functions having different levels about reliability. Therefore, the reliability optimization allocation only considering cost constraint conditions is not accurate and will results in disaccord between the obtained results with actual situation. Focusing on the problem mentioned above, a reliability optimization allocation method that considers cost constraint and importance factor is proposed. In this paper, we consider systems consisting of units characterized by different reliability and importance factors. Such systems are multi-function because they must perform different tasks depending on the combination of units. Different functions may work simultaneously. Firstly, the concept of importance factor is defined to describe the importance of a unit and the required importance factor level of system functions in the task is also given. To deal with the differentiation of system functions, the corresponding bound about importance factor are executed when looking for the optimal solution. Similarly, the cost constraint is also forced. Finally, in order to reduce the randomness of intelligent algorithm, a number of optimization are conducted and a rule is proposed to select the most optimal solution from all the optimal solutions which are obtained in every iterative loop. Example of an integrated transmission device is presented. To begin with, we establish the reliability function of system as the objective optimization function. Then, the restraint of budget and different demands of importance factor of system functions are posed. Furthermore, using a genetic algorithm as the optimization tool, the optimization result can be obtained. Finally, the most optimal solution is selected. The results show that, the method, we proposed is more correct and more approximate than the reality. To verify the advantages and engineering applicability of the new method, the results obtained by the new method are compared with the results obtained under different conditions using basic genetic algorithm, without considering functions and the differentiation of functions, to solve the allocation problem of integrated transmission device, respectively. The reliability optimization allocation method presented in this paper can not only consider the constraint of cost but also can consider the diversities of functions, and thus the optimization results will be more approximate in actual situation. At the same time, this paper can also provide guidance for the similar reliability optimization problem.