Abstract The population density of Père David’s deer (Elaphurus davidianus) in Jiangsu Dafeng Milu Nature Reserve was excessively high due to an overemphasis on population recovery, while ignoring the crucial relationship between population size and habitats. This study used immunocastration to capture four Père David’s deer and observed their behavior. Their blood was collected for sex hormone testing, transcriptomics, and metabolomics analysis. In addition, six uncastrated Père David’s deer were included as control group. The results showed that reproductive behavior was absent in castrated Père David’s deer, while castrated individuals exhibited a significant decrease in blood hormone testosterone concentration compared to uncastrated Père David’s deer. Transcriptome and metabolome analyses revealed 450 differentially expressed genes (DEGs) and five differentially expressed metabolites (DEMs), Combined analysis of transcriptome and metabolic data revealed a significant correlation between DEGs and DEMs. It shows that using immune castration to control the population of Père David’s deer may disrupt their cell apoptosis and disturb the cell cycle, leading to abnormal pathways and promoting the onset of many diseases. Therefore, a cautious approach should be adopted toward immune castration as a means of population control. This study can provide valuable references for the standardized management of Père David’s deer populations.