Modularization is an important method of software development. Developing modules requires a certain cost. In order to ensure the system trustworthiness goal, additional cost is required. Therefore, how to allocate cost to each module to optimize software trustworthiness within the development cost given by users is an important research issue. Firstly, according to the relationship between module trustworthiness and cost, the cost estimation model of module trustworthiness is established. Secondly, based on different combination ways of modules, software trustworthiness and cost allocation models under different structures of software system are established and corresponding allocation algorithms are designed by using dynamic programming. Within the development cost given by users, the proposed allocation algorithms can allocate the development cost to each module, so as to optimize the software system trustworthiness. Finally, a case of automatic ticketing system shows the feasibility of the proposed allocation algorithms.