Scaffolds composed of polymers and nano-hydroxyapatite (n-HA) have received extensive attention in bone reconstructive repair; however there is a lack of in-depth and long-term comparative study on the effect of scaffold degradability on bone reconstruction. In this study, the osteogenic behaviors of three polymeric composite scaffolds based on fast degradable poly(lactic-co-glycolic acid) (PLGA), slowly degradable polycaprolactone (PCL) and non-degradable polyamide 66 (PA66) were investigated and compared via implanting the scaffolds into rabbit femoral defects for 1, 3, 6 and 12 months. The in vivo results demonstrated that although the n-HA/PLGA scaffold could obtain higher new bone volume at 3 months, its fast degradation caused the loss of scaffold structural integrity and led to reduction of bone volume after 3 months. The n-HA/PCL scaffold displayed slow degradation mainly after 6 months (∼20% degradation) and the n-HA/PA66 scaffold showed no degradation during the entire 12 months; these two scaffolds could maintain their structural integrity and exhibited a constant increase in bone volume with the implantation time, and even achieved higher bone volume than the n-HA/PLGA scaffold at 12 months. The year-long in vivo research revealed the following important aspects: (1) bone reconstruction is strongly related to scaffold degradability, and the scaffold structural integrity should be maintained at least for one year before complete degradation in vivo; (2) the in vivo experiment of a bone scaffold must take more time than the conventional 3 or 6 months, which is normally neglected. The study suggests a principle for future design and application of bone scaffolds that must have a relatively stable osteogenic space and scaffold interface, or have a scaffold degradation speed slower than the time of bone reconstruction completion.