Taiwan has experienced an increase in the frequency of heavy rainfall, droughts, and floods in recent years, making green onion plants more prone to stem rot, leaf blight, and even widespread death. At first, people thought that the heavy rain and flooding led to poor growth, but according to TARI’s research, most of these losses were caused by a kind of microorganism, Phytophthora nicotianae Breda de Haan. Based on the artificial environment simulation test, we preliminarily concluded that the conditions, under which the disease of Taiwan’s green onion is prone to occur in summer and autumn, are overcast and rainy for more than two consecutive days. Because the disease cannot be eradicated by chemical pesticides alone, integrated pest management could be applied to control the disease, including no-Phytophthora contaminated green onion suckers, rational fertilization, weekly-spraying neutralized phosphite acid solution once every 2 weeks about 2 months before heavy rainfall, as well as fungicide-spraying 7 days or less and 1 day before the heavy rainfall. These crop health management measures could significantly reduce the occurrence of disease and yield loss.During a continuous drought period, the green onion is prone to insects, particularly beet armyworm, Spodoptera exigua. Green onion fields in the same region can hang beet armyworm pheromone traps together to trap and kill male moths and monitor the number of armyworms. When the number of insects exceeds the warning limit, the number and pesticide resistance of beet armyworm can be reduced by the timely application of Bacillus turingiensis and the rotation of different classes of pesticides. Furthermore, the institute found that the treatment of green onion seedlings with Bacillus amyloliquefaciens T33SR2 can greatly reduce the root nodulation caused by root-knot nematodes during the cultivation process. If green onion plants are regularly sprinkled with relatively safe and low-risk hypochlorous acid solution, the damage caused by bacterial soft rot can also be reduced.