Animal ethics mainly discusses the problem of how mankind treats animals, which is related to the existence of moral position of animals and the discussion of animal interest value. Animal Welfare Theory is one of the descriptions of contemporary animal ethics, which is approved by Taiwan and serves as the basic interest of protecting animals. Because “animal welfare theory” is originated from the West, the lack of understanding the history of how the westerners protected the animals and its real meaning caused the protection towards laboratory animals in Taiwan becomes unpractical. For this reason, this study traced back to the historical background and incident meaning of “Christianity”, “science”, “ethics”, and “animal experiment” in the West to explain the conception, meaning, and purpose of “welfare theory” on protecting laboratory animals. The essential contents of Animal Protection Act in Taiwan were cross-compared with the viewpoints of welfare theory. This study found that four problems were hidden in laboratory animal protection mechanism of Taiwan: First, the species and subjects protected by Animal Protection Act were significantly insufficient, and this Act was unable to manifest the essence of the five freedoms and the 3 Rs. Second, the ethics supervision mechanism of laboratory animals could not show its supervision and audit efficiency timely because of the defects of system design. Third, for the medical treatment, supervision, and euthanasia of the laboratory animals, veterinarian does not mandatorily need to participate, causing negligence when implementing the welfare. Fourth, the protection towards laboratory animals and companion animals during the implementation and punishment of administrative supervision showed significant difference. Last but not least, methods to improve the above-mentioned defects were proposed.