The need for an efficient sampling technique to collect aquatic organisms has risen with the increase of interest in rice paddy fields, which have been recognized as important ecosystems supporting biodiversity. In the present study, a submerged funnel trap used with the assistance of attracting agents (fish meal and chemical light) was designed as an easy, objective and quantitative tool for collecting aquatic organisms in the rice paddy fields. The preference for collecting aquatic organisms as a means for attracting agents was analyzed using a generalized linear mixed model. Also, based on the data of previous research, we compared the community composition of the aquatic macroinvertebrates, which were collected using the quadrat method, and newly designed submerged funnel traps, by analyzing non-metric multidimensional scaling. The results showed that the catching efficiency of 18 of the total 65 taxa was affected by the attracting agents. 12 taxa including Pomacea canaliculata, Hippeutis cantori, Austropeplea ollula, Erpobdella lineata, Ostracoda spp. Branchinella kugenumaensis, Hydaticus grammicus, Rhantus pulverosus, Chironomidae spp., Rana nigromaculata, Cobitidae spp. etc., favored fish meal and 6 taxa including Ischnura asiatica, Coenagrionidae spp. Sternolophus rufipes etc., were attracted by chemical light. The submerged funnel trap used as a measurement tool for biodiversity was less applicable than the quadrat method; however, it was more effective for the selective collection of specific taxa. We expect that this newly designed trap can be a simple and quantitative method for collecting aquatic organisms, and could be used for long term and extensive surveys in rice paddy fields in the future.