Recent methods that integrate spatial layouts with text for document understanding in large language models (LLMs) have shown promising results. A commonly used method is to represent layout information as text tokens and interleave them with text content as inputs to the LLMs. However, such a method still demonstrates limitations, as it requires additional position IDs for tokens that are used to represent layout information. Due to the constraint on max position IDs, assigning them to layout information reduces those available for text content, reducing the capacity for the model to learn from the text during training, while also introducing a large number of potentially untrained position IDs during long-context inference, which can hinder performance on document understanding tasks.To address these issues, we propose LayTokenLLM, a simple yet effective method for document understanding. LayTokenLLM represents layout information as a single token per text segment and uses a specialized positional encoding scheme. It shares position IDs between text and layout tokens, eliminating the need for additional position IDs. This design maintains the model's capacity to learn from text while mitigating long-context issues during inference. Furthermore, a novel pre-training objective called Next Interleaved Text and Layout Token Prediction (NTLP) is devised to enhance cross-modality learning between text and layout tokens. Extensive experiments show that LayTokenLLM outperforms existing layout-integrated LLMs and MLLMs of similar scales on multi-page document understanding tasks, while also achieving superior performance on most single-page tasks. Code and data will be publicly available.