The rapid development of transgenic biotechnology has greatly promoted the commercialization of genetically modified (GM) crops including the insect-resistant crops worldwide. Apart from the enormous yield benefits brought by the GM crops, the cryptic fitness cost associated with transgenes has also been detected under experimental conditions although it is considered to be rare. To estimate the yield benefit and cost of insect-resistant GM rice, we studied field performances of three insect-resistant GM rice lines, involving their non-GM parental variety as comparison. Great benefits as estimated by the yield-related traits were observed in the GM rice lines when high insect pressure was recorded, but a cryptic yield loss was detected when the level of insect pressure was extremely low. Given the fact that cryptic yield loss presented in the GM rice lines under the low insect pressure, a strategic field deployment should be required when insect-resistant GM rice are commercialized to circumvent the unnecessary yield losses. This is probably true for other insect-resistant GM crops. Effective biotechnology and breeding measures are also needed to particularly minimize the potential underlying cost of an insect-resistance transgene before commercial production of the GM crops.