Large Reasoning Models(LRMs) such as OpenAI o1 and DeepSeek-R1 have shown remarkable reasoning capabilities by scaling test-time compute and generating long Chain-of-Thought(CoT). Distillation--post-training on LRMs-generated data--is a straightforward yet effective method to enhance the reasoning abilities of smaller models, but faces a critical bottleneck: we found that distilled long CoT data poses learning difficulty for small models and leads to the inheritance of biases (i.e. over-thinking) when using Supervised Fine-tuning(SFT) and Reinforcement Learning(RL) methods. To alleviate this bottleneck, we propose constructing tree-based CoT data from scratch via Monte Carlo Tree Search(MCTS). We then exploit a set of CoT-aware approaches, including Thoughts Length Balance, Fine-grained DPO, and Joint Post-training Objective, to enhance SFT and RL on the construted data.