This study demonstrates cross-linking-filler composites in which covalent bonds between the fillers and polymer chains act as the main cross-linking points for the development of flexible and thermally conductive materials. Cross-linking-filler composites are fabricated using functionalized hexagonal boron nitride (hBN) fillers and polyrotaxane, called slide-ring polymers. The hBN particles modified with a carbon layer were produced by plasma processing in hydroquinone aqueous solution and functionalized with isocyanate groups. As the functionalized hBN provides cross-linking points for polyrotaxane, the cross-linking-filler composites can reduce cross-linking agents among polyrotaxane and exhibit considerable flexibility. Young's moduli of the cross-linking-filler composites are much lower than those of previously reported polyrotaxane composites while retaining their toughness. These values are relatively close to those of unfilled polyrotaxane elastomers, despite containing hBN fillers with a content of 50 wt %. Thus, the cross-linking-filler composites exhibit a combination of flexibility and thermal conductivity, which few hBN/elastomer composites have achieved.