This paper presents the Implicit Knowledge Distillation Diffusion Transformer (IKDDiT), a groundbreaking model tailored for photolithography overlay map generation in semiconductor manufacturing. IKDDiT effectively addresses the challenges of open-vocabulary overlay map generation by integrating pre-trained image-text encoders, diffusion models, and masked transformers. Utilizing advanced text-to-image diffusion and image-text discriminative models, it generates high-fidelity overlay maps across multiple photolithography layers, significantly mitigating overlay misregistration errors and minimizing productivity losses caused by wafer rework. Key innovations include an implicit knowledge distillation framework that refines inter-image alignment by decoupling discriminative and generative tasks via an implicit discriminator, as well as a gated cross-attention mechanism to enhance generative performance. Experimental results demonstrate that IKDDiT achieves an optimal trade-off between efficiency and accuracy, providing a scalable, robust solution poised to advance overlay map generation in semiconductor processes.