Ionic liquids (ILs) become emerging environmental pollutants. Especially, alkyl imidazolium ILs commonly showed stimulation in toxicological studies and mechanisms remained to be explored. In the present study, alkyl imidazolium tetrafluoroborate ([amim]BF4), with ethyl ([emim]), hexyl ([hmim]) and octyl ([omim]) as side-chains, were chosen as target ILs. Their toxicities on the reproduction and lifespan of Caenorhabditis elegans were explored with two types (A and B) exposure arrangements to mimic realistic intermittent multi-generational exposure scenarios. In type A scenario, there was an exposure every 4 generations with 12 generations in total, and in type B one, there was an exposure every two generations with 12 generations in total. Result showed that [emim]BF4 caused inhibition on the reproduction in 8 generations in type A exposure but 6 ones in type B exposure. Meanwhile, [hmim]BF4 showed inhibition in one generation and stimulation in 3 generations in type A exposure, but stimulation in 6 generations in type B exposure. Also, [omim]BF4 showed stimulation in one generation in type B exposure. Collectively, the results demonstrated less frequencies of inhibition, or more frequencies of stimulation, in the exposure scenario with more frequent exposures. Further mechanism exploration was performed to measure the lipid storage and metabolism in the aspect of energy supply. Results showed that [emim]BF4, [hmim]BF4 and [omim]BF4 commonly stimulated the triglyceride (TG) levels across generations. They also disturbed the activities of glycerol-3-phosphate acyltransferase (GPAT) and acetyl CoA carboxylase (ACC) in lipogenesis, those of adipose triglyceride lipase (ATGL) and carnitine acyl transferase (CPT) in lipolysis, and also the contents of acetyl-CoA (ACA). Further data analysis indicated the energy allocation among life traits including reproduction, antioxidant responses and hormone regulations.