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We aimed to evaluate the materials based on 4‐methacryloxyethyl trimellitate anhydride/methyl methacrylate tri‐n‐butylborane (Super‐bond [SB]) and nano hydroxyapatite (naHAp) for the repair of perforation at pulp chamber floor (PPF) in vitro and in vivo models. SB and naHAp were mixed in the mass ratio of 10% or 30% to produce naHAp/SB. Human periodontal ligament stem cells (HPDLSCs) were cultured on resin discs of SB or naHAp/SB to analyze the effects of naHAp/SB on cell adhesion, proliferation, and cementoblastic differentiation. A rat PPF model was treated with SB or naHAp/SB to examine the effects of naHAp/SB on the healing of defected cementum and periodontal ligament (PDL) at the site of PPF. HPDLSCs were spindle‐shaped and adhered to all resin discs. Changing the resin from SB to naHAp/SB did not significantly alter cell proliferation. Both 10% and 30% naHAp/SB were more effective than SB in promoting cementoblastic differentiation of HPDLSCs. In the rat PPF model, 30% naHAp/SB was more effective than SB in promoting the formation Sharpey's fiber‐like structures with expression of the PDL‐related marker and cementum‐like structures with expression of cementum‐related markers. In conclusion, 30% naHAp/SB can be the new restorative material for PPF because it exhibited the abilities of adhering to dentin and healing of defected periodontal tissue. Significance Statement: Perforation at pulp chamber floor (PPF) induces inflammatory reactions in surrounding periodontal tissues and leads to tooth loss. An ideal restorative material should exhibit biocompatibility, provide an adequate bond strength to dentin, and induce the healing of defected periodontal tissues. However, the materials meet all requirements were not reported. We aimed to develop and evaluate new materials based on 4‐methacryloxyethyl trimellitate anhydride/methyl methacrylate tri‐n‐butylborane (super‐bond [SB]) and nano hydroxyapatite (naHAp) and mixed them (naHAp/SB). The naHAp/SB exhibited biocompatible properties with adhering ability to dentin and induced the healing of natural periodontal tissues. Our results suggested that naHAp/SB may be the new material meeting all requirements for the repair of PPF and it seems to lead to long‐term preservation of tooth. [ABSTRACT FROM AUTHOR]