Nanoattapulgite (nano-ATP), a magnesium-aluminum silicate clay, can absorb substances and is a suitable material for bone repair and regeneration. In this study, using three-dimensional printing technology, a nano-ATP/polycaprolactone (PCL) scaffold was fabricated and modified using NaOH to form a rough surface. Biomimetic hydroxyapatite (HA) on nano-ATP/PCL scaffolds was fabricated using a biomineralized approach. The scaffold provided structural support through PCL and was modified with ATP and HA to improve hydrophilicity and promote the delivery of nutrients. The biocompatibility and osteogenic induction of scaffolds were assessed in vitro using mouse bone marrow mesenchymal stem cells. According to the in vitro study results, the nano-ATP/PCL/HA composite scaffold significantly boosted the expression levels of genes related to osteogenesis (p < 0.05), attributed to its superior alkaline phosphatase activity and calcium deposition capabilities. The outcomes of in vivo experimentation demonstrated an augmentation in bone growth at the rat cranial defect site when treated with the ATP/PCL/HA composite scaffold. It can be inferred from the results that the implementation of ATP and HA for the bone tissue engineering repair material displays encouraging prospects.