Construction site layout plans (CSLP) are crucial for efficient prefabricated construction project management. Traditional manual design process is costly and time-consuming, while optimization methods heavily depend on expert knowledge. Recent advancements in deep generative models present promising alternatives. However, their application to the generation of prefabricated construction site layouts is hindered by several challenges, including limited datasets, significant overlap between facilities, and the necessity to generate layouts based on fixed facilities with specific attributes such as minimal transportation costs. These challenges constrain the efficacy and applicability of the generated layouts. To address these issues, this study introduces an innovative automated generative design system for prefabricated construction site layouts, leveraging a novel Transformer-based conditional generative adversarial network (GAN). The data preparation module of the system collects and augments layout data for training. The CSLGAN module is designed to generate layouts that conform to spatial constraints and desired attributes, with minimal facility overlap. Furthermore, this study establishes benchmarks in terms of model capacity and specialized performance metrics. Extensive experiments demonstrate the effectiveness of the proposed system in automated construction site layout generation.