The paper examined the effect of automation on organisational structure, job performance and communication in university libraries in South West, Nigeria. The survey research design was adopted. A questionnaire and observation checklist was the instrument used to collect the data. The sample for the study consisted of 607 library personnel in six (6) university libraries in South West, Nigeria, stratified and judgemental sampling was used to sample 442 library staff for the study. Descriptive statistics were used to analyse data collected on the research questions developed while for inferential statistics, Kendall-tau was used to test hypotheses. Findings from the study revealed that none of the university libraries studied has been to implement full automation of their operations, only acquisitions have been automated across the board in the four (4) university libraries. Also, the findings revealed that automation has enabled a more flexible working environment, affected the pattern of staffing by specialisation, and bridged the gap between communication flow through the use of a variety of information and technology communication (ICT) tools. Furthermore, the study identified that the various constraints to automation in university libraries are irregular power supply, inadequate funding, lack of infrastructural facilities, and staff resistance to training. The study recommended that university and library management of the university libraries studied should make provision for full automation of library operations and services. This will go a long way in adopting new structures in line with technological advancements for greater flexibility, facilitating staff creativity at work, help improve collaboration and resource sharing through the use of automation tools for communication.