The pre-training paradigm plays a key role in the success of Large Language Models (LLMs), which have been recognized as one of the most significant advancements of AI recently. Building on these breakthroughs, code LLMs with advanced coding capabilities bring huge impacts on software engineering, showing the tendency to become an essential part of developers' daily routines. However, the current code LLMs still face serious challenges related to trustworthiness, as they can generate incorrect, insecure, or unreliable code. Recent exploratory studies find that it can be promising to detect such risky outputs by analyzing LLMs' internal states, akin to how the human brain unconsciously recognizes its own mistakes. Yet, most of these approaches are limited to narrow sub-domains of LLM operations and fall short of achieving industry-level scalability and practicability. To address these challenges, in this paper, we propose PtTrust, a two-stage risk assessment framework for code LLM based on internal state pre-training, designed to integrate seamlessly with the existing infrastructure of software companies. The core idea is that the risk assessment framework could also undergo a pre-training process similar to LLMs. Specifically, PtTrust first performs unsupervised pre-training on large-scale unlabeled source code to learn general representations of LLM states. Then, it uses a small, labeled dataset to train a risk predictor. We demonstrate the effectiveness of PtTrust through fine-grained, code line-level risk assessment and demonstrate that it generalizes across tasks and different programming languages. Further experiments also reveal that PtTrust provides highly intuitive and interpretable features, fostering greater user trust. We believe PtTrust makes a promising step toward scalable and trustworthy assurance for code LLMs.