Farming practices that balance environmental friendliness with biodiversity are increasingly valuable. Wild plants on farmlands compete for nutrients with crops and create a crucial microhabitat and resources for animals such as natural enemies. Investigating farmlands and their surrounding plants with limited human and material resources has become an essential aspect of evaluating the agricultural ecosystem services. This study investigated plants in six agricultural long-term ecological research sites in Taiwan from 2017 to 2020 to determine the ideal season for investigation. Cluster analysis was performed to group habitats with similar plant composition, and the species–area curves of the clusters in each season were created. The results indicated that the agricultural ecosystem could be divided into farmlands, banks, orchards, and tea gardens. The habitats were divided into farmland, bank, Chia-Yi orchard, Gu-Keng orchard, and tea garden clusters. Ground plant cover can be investigated all year with at least 18 quadrats. However, if human and material resources are limited, 10 quadrats should be the minimum for farmlands in autumn and for the other microhabitats in spring. The minimum number of quadrats is 10 for banks, 17 for orchards, and 9 for tea gardens.