The traditional overwintering process of sea cucumbers (Apostichopus japonicus) requires burning a large amount of coal to raise the water temperature. It is useful but costly and not environmentally friendly. Bacillus is proposed as a cheap and green alternative. Therefore, this study intended to achieve cleaner production of A. japonicus by adding Bacillus to their diet at low temperature (7 °C) to achieve the production efficiency of sea cucumbers cultured by heating water to 11 °C. Here, we found that number of crawl steps, relative food intake, relative fecal outputs, amylase and proteinase activities, body weight and weight gain rate significantly reduced, and intestinal morphology and intestinal microbiota were also worse in sea cucumbers at low temperature (7 °C), compared with the sea cucumbers cultured at 11 °C. This suggests that low temperature negatively affect the behaviors, intestinal health, and growth of A. japonicus. However, the adverse effects on the behavioral capacities (such as number of crawl steps, relative food intake and relative fecal outputs), intestinal health (such as digestive enzyme activities and intestinal morphology), and growth (such as body weight and weight gain rate) of sea cucumbers under low temperature conditions were compensated after adding dietary Bacillus (Bacillus methylotrophicus and Bacillus amyloliquefaciens) at 10