[Purposes] This study offers a solution for integrated processing of two-dimensional codes in scientific journals with Computer Systems and Applications as an example to make the process more operable, reliable, and efficient, which is expected to serve as a reference for other journals. [Methods] We first summarized and analyzed the common problems in manual processing of two-dimensional codes, then designed the integrated processing tool for two-dimensional codes using Python language, and compared it with the manual processing. [Findings] The integrated tool can realize the automatic generation, insertion, and verification of two-dimensional codes. Taking Computer Systems and Applications as an example, manual processing of two-dimensional codes in 45 papers takes about 2 hours, while the automatic processing only costs about 30 seconds with no error. The verification of two-dimensional codes by the integrated tool is independent of the websites, thus smoothing the traditional publishing process in the presence of two-dimensional codes. [Conclusions] The proposed solution can deal with two-dimensional codes in scientific journals with high efficiency and accuracy. Computer automation boasts higher efficiency and reliability in dealing with repetitive work. Editors of scientific journals should think more about the publishing process and constantly improve work efficiency and workflow with the help of computer technology.