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Insect quantity is an important index for determining the degree of damage to plants. The brown planthopper (BPH), Nilaparvata lugens (St?l), is one of the most important rice pests in Asia. Here, we used two genotypes of BPH, a high-fecundity genotype (HFG) and a low-fecundity genotype (LFG), to measure their ecological fitness and to explore possible causes for genotype differentiation by transcriptome sequencing. Our results showed that there were significant differences in body weight, egg hatching rate and honeydew secretion between the HFG and LFG, particularly, the number of eggs laid per female was more significant. Transcriptional analysis showed that a total of 1966 differentially expressed genes (DEGs) were mainly involved in energy metabolism, carbohydrate and lipid synthesis, insect hormone synthesis and fecundity-related pathways. Moreover, we found that the phosphorylation levels of AMPK, AKT and FoxO and the synthesis of ecdysone were different between the two genotypes of BPH. These findings may partially explain the difference in the ecological fitness between HFG and LFG. This study is the first to compare the differences between two genotypes of BPH and to provide transcriptomic evidence to further understand the fecundity of BPH.