The deterioration risk of bale silage is relatively high because of a high surface-area to volume ratio. Therefore, the damages of plastic covers of bales should receive particular attention since it may often occur during removing or transportation process. When bales are punctured, oxygen is allowed to permeate the silage and subsequently aerobic organisms flourish and metabolize the products of fermentation, and the temperature inside the bales will rise up again. So temperature is a key indicator when the material is noticed to be “heating” since while oxygen comes into contact with the silage. In order to forecast the risks of aerobic deterioration of silage, grass bale silage and alfalfa bale silage were selected as study objects. The method which used to embed temperature sensors into the bale to measure the temperature was proposed. The self-developed multi-sensor experimental system with a specific penetration shaft and cone (V-structure) was used. While the cone penetrated into bale, the thermal-couple sensor followed the cone into the bale. If the cone arrived at the place desired, the cone would extract but the thermal sensors would stay at the place. It can put the sensors into bale without introducing air followed. Two schemes measuring temperature changes in punctured bale were designed. The temperature of planned locations in bale was monitored. It was detected that the temperature of the silage which was closer from the damaged cover rose sooner. Paired t test was done between the corresponding values from the upper and the lower within bale silage. The test results showed that two temperature rising processes of upper and lower had a significant difference. By temperature curve comparison of the same silage materials with different dry matter contents, it was found that the temperature rising of silage with higher dry matter was faster. Furthermore, to measure the temperature field inside bale, a specific penetrometer was designed. It was fixed on the platform of measurement and controlled during temperature measurement. Based on the data of temperature distribution, the temperature distribution in bale silage could be visualized in 3D map. It is a powerful tool to analyze temperature distribution around the bale silage in multi-angle.