Over the past 14 years, the chemical hybridization agent SQ-1 (CHA-SQ-1) has been widely used for inducing male sterility in wheat heterosis in China. However, any indirect effects of CHA-SQ-1 on high trophic level of food chains (e.g., wheat pests) have not been tested. Therefore, we addressed the question, under laboratory conditions, by firstly rearing the first generation of two Sitobion avenae clones on wheats sprayed with either CHA-SQ-1 or distilled water. Then, the population parameters of the corresponding offspring of the two clones, living on wheat leaves without CHA-SQ-1, were examined across two generations. The results showed that CHA-SQ-1 significantly decreased the intrinsic rate of increase (r), net reproductive rate (R-0), and finite rate of increase (lambda) but not the mean generation time (T) in the aphid Kunming clone. However, in the Tianjin clone, CHA-SQ-1 clearly reduced the mean generation time (T) but not the other population parameters. These results demonstrated that CHA-SQ-1 could decelerate the growth of S. avenae populations. Additionally, the interaction was significant between aphid genotype and treatment (CHA-SQ-1) on these population parameters. The study will increase the understanding of CHA-SQ-1 on the ecological safety evaluation and pest control.