The intercalation strategy has become crucial for 2D layered materials to achieve desirable properties, however, the intercalated guests are often limited to metal ions or small molecules. Here, we develop a simple, mild and efficient polymer-direct-intercalation strategy that different polymers (polyethyleneimine and polyethylene glycol) can directly intercalate into the MoS₂ interlayers, forming MoS²-polymer composites and interlayer-expanded MoS₂/carbon heteroaerogels after carbonization. The polymer-direct-intercalation behavior has been investigated by substantial characterizations and molecular dynamic calculations. The resulting composite heteroaerogels possess 3D conductive MoS₂/C frameworks, expanded MoS₂ interlayers (0.98 nm), high MoS₂ contents (up to 74%) and high Mo valence (+6), beneficial to fast and stable charge transport and enhanced pseudocapacitive energy storage. Consequently, the typical MoS₂/N-doped carbon heteroaerogels exhibit outstanding supercapacitor performance, such as ultrahigh capacitance, remarkable rate capability and excellent cycling stability. This study offers a new intercalation strategy which may be generally applicable to 2D materials for promising energy applications.