The remarkable success of Chain-of-Thought (CoT), which enhances performance by scaling generation steps at test-time, inspires us to ask: can we leverage a similar scaling of computational steps during pretraining to improve the generation of each individual token? To address this, we propose a novel pre-training methodology: Pretraining Language Models with Latent Thoughts (PonderLM-2). Our approach pretrains a language model (LM) to first generate an intermediate latent thought-the last hidden state of the current position-which is then used as input to predict the actual subsequent token. This additional computational step enables the LM to refine its prediction within unconstrained continuous space. Our experiments demonstrate that, at an identical inference cost, a LM that generates one additional latent thought per token outperforms a standard model with double the parameters. For instance, our PonderLM-2-Pythia-1.4B, pretrained on 300B tokens from the Pile, significantly surpasses the vanilla Pythia-2.8B trained on the same data on both language modeling and a range of general downstream tasks. Furthermore, increasing the number of latent thoughts generated before each actual token-forming a chain analogous to CoT-consistently improves the model's performance. The code is available at https://github.com/LUMIA-Group/PonderLM-2.