Large language models (LLMs) face inherent performance bottlenecks under parameter constraints, particularly in processing critical tokens that demand complex reasoning. Empirical analysis reveals challenging tokens induce abrupt gradient spikes across layers, exposing architectural stress points in standard Transformers. Building on this insight, we propose Inner Thinking Transformer (ITT), which reimagines layer computations as implicit thinking steps. ITT dynamically allocates computation through Adaptive Token Routing, iteratively refines representations via Residual Thinking Connections, and distinguishes reasoning phases using Thinking Step Encoding. ITT enables deeper processing of critical tokens without parameter expansion. Evaluations across 162M-466M parameter models show ITT achieves 96.5% performance of a 466M Transformer using only 162M parameters, reduces training data by 43.2%, and outperforms Transformer/Loop variants in 11 benchmarks. By enabling elastic computation allocation during inference, ITT balances performance and efficiency through architecture-aware optimization of implicit thinking pathways.