Ecological engineering has become a promising strategy for restoring paddy field biodiversity and enhancing yield. This study aims to evaluate the effectiveness of refuge plants and cropping systems on the population of useful arthropods and rice production. The study was conducted on a paddy field in Central Sulawesi, Indonesia, using a Split Plot Design. The main plots were refuge plants with four treatments, namely rice without refuge crops, rice crops with wild Cosmos (C. caudatus), marigold (Tagetes erecta), and both flower plants as the refuges, whereas two cropping systems, i.e., the jajar legowo system (JLS) of 2:1 and the symmetries system (SS) was set up as a sub-plot. Direct observation and collection of the arthropods were carried out using yellow-pan traps and a sweep net. The parasitoid eggs were reared at the laboratory. In addition, rice growth and yields were measured. The refuge plants and cropping system had no significant effects on the overall arthropods population but changed their diversity and community structure and increased the proportion of useful arthropods as well. Meanwhile, rice production in the JLS (5.16 tons GKG ha−1) was significantly higher than those of the SS (4.10 tons GKG ha−1), and this was in line with the differences in the panicles number in both cropping systems. The study highlighted the importance of the implementation of ecological engineering at the paddy fields by using the flower plants as the refuge and food sources for the beneficial organisms combined by JLS for enhancing the rice yields.