Metal-organic frameworks (MOFs) derived magnetic carbon-based nanocomposites have drawn widespread attentions due to the well distributed nanocrystals in carbon matrix. Dynamically observing the formation process is urgently needed. Herein, taking zeolitic imidazolate framework (ZIF)-67 as an example, the pyrolysis process is investigated by in-situ transmission electron microscopy (TEM) assisted with ex-situ characterizations. Co nanocrystals are evenly distributed in carbon at the initial stage of carbonization. By increasing pyrolysis temperature, the nanocrystals grow bigger and migrate to carbon surface. The carbon texture transfers from amorphous to crystalline at 600 °C, and thoroughly converts at 800 °C. In-situ heating TEM shows that more tiny Co nanocrystals move out from the carbon texture by increasing temperature from 700 to 800 °C. At 1,000 °C, some escaped tiny Co nanocrystals are volatilized and disappeared. The residual escaped Co nanocrystals catalyze the formation of carbon nanotubes (CNTs). Due to the synergistic effect between Co and carbon as well as porous structure, the nanocomposites show high-efficient microwave absorption performance, which can be tuned by pyrolysis temperature, heating rate, and mass fraction. When the mass fraction is 30 wt.%, the nanocomposites obtained at 600 or 700 °C display remarkable microwave absorption with optimal reflection loss (RL) smaller than −70 dB and effective absorption band larger than 4.9 GHz. Combining the in-situ and ex-situ techniques, some key findings were observed: (1) graphitization of carbon; (2) volatilization of Co nanocrystals; (3) formation process of CNTs by Co catalyst. These findings are helpful to understand the formation of MOFs derived carbon-based composites and expand their practical applications, especially for microwave absorption.