The cytocompatibility of biological and synthetic materials is an important issue for biomaterials. Gelatin hydrogels are used as biomaterials because of their biodegradability. We have previously reported that the mechanical properties of gelatin hydrogels are improved by cross-linking with polyrotaxanes, a supramolecular compound composed of many cyclic molecules threaded with a linear polymer. In this study, the ability of gelatin hydrogels cross-linked by polyrotaxanes (polyrotaxane–gelatin hydrogels) for cell cultivation was investigated. Because the amount of polyrotaxanes used for gelatin fabrication is very small, the chemical composition was barely altered. The structure and wettability of these hydrogels are also the same as those of conventional hydrogels. Fibroblasts adhered on polyrotaxane–gelatin hydrogels and conventional hydrogels without any reduction or apoptosis of adherent cells. From these results, the polyrotaxane–gelatin hydrogels have the potential to improve the mechanical properties of gelatin without affecting cytocompatibility. Interestingly, when cells were cultured on polyrotaxane–gelatin hydrogels after repeated stress deformation, the cells were spontaneously oriented to the stretching direction. This cellular response was not observed on conventional hydrogels. These results suggest that the use of a polyrotaxane cross-linking agent can not only improve the strength of hydrogels but can also contribute to controlling reorientation of the gelatin.