Senile osteoporosis (SOP) is a related disease of systematic degenerative changes in bones during natural aging. Increasing age is an important factor in its pathogenesis. This experiment was to evaluate the comprehensive effect of calcium with vitamin D3 (CaD) on SOP based on multilayer perception (MLP)–artificial neural network (ANN) methods. 15-month-old male Sprague-Dawley rats were administered CaD for 2 months, while 3-, 6-, 9-, 12-, 15- and 17-month-old rats were used as the mature or aging control groups. We detected the bone mass and bone mineral density (BMD), performed biomechanical testing and measured micro-CT properties to evaluate the degree of osteoporosis. Levels of alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRACP), and the ratio of ALP to TRACP both in serum and bone were measured for the evaluation of the bone turnover rate. The bone mRNA and protein expression of ATP6v0d2, IGF-1, BMP2, M-CSF, Wnt5a and TGF-β1 were detected by western blotting (WB), immunofluorescence (IF) and quantitative real time polymerase chain reaction (qRT-PCR) for evaluating bone metabolism in the bone microenvironment. The MLP–ANN model was constructed and used to evaluate the importance of related parameters and the comprehensive action of CaD. Our data showed that bone mass, BMD, maximal load, ultimate displacement, ALP and TRACP in serum and tibia, and the protein and mRNA expressions of ATP6v0d2, IGF-1, BMP2, M-CSF, Wnt5a and TGF-β1 in tibia reached a peak in 6 m rats, and then were gradually decreased with the increase of age to the lowest in 17 m rats. This study demonstrated the degeneration of the bone structure and bone metabolism in SOP rats during the aging process of rats aged 3 to 17 months. CaD could effectively increase bone mass and bone strength, alleviate the degradation of the bone microstructure and rebalance bone remodeling. In addition, the MLP model was a comprehensive method for evaluating the effects of drugs on SOP, which provided a new direction for future drug and nutrition evaluation.