Abstract: With the rapid development of tropical-specific and efficient agriculture coupled with changes in planting structures, the uncertainty regarding the implications of new farming management patterns on vegetable ecosystems has heightened. As important indicators for assessing soil quality, soil microorganisms play a crucial role in maintaining soil function. Therefore, monitoring microbial community composition and function and metabolism under the cropping system in tropical region is particularly important for investigating microbial community successions and their driving factors and unraveling intricate processes like nutrient cycling and other microscopic mechanisms.. Based on soil microbial DNA/RNA molecular biology techniques, this dataset was integrated with high-throughput sequencing data of soil bacteria and fungi under three fertilization patterns: chemical fertilizer alone, straw return, and chemical fertilizer + straw return in vegetable fields in Wenchang City, Hainan Province during 2016-2021. The processes of site setting, observation and maintenance, sample collection, sample preparation and preservation, data filling and quality control are strictly implemented in accordance with the unified standards of China Ecological Research Network (CERN). The dataset is of great significance for studying the nutrient cycling of vegetable ecosystems in tropical regions, analyzing the interaction mechanism between environmental elements and production systems, adjusting crop cultivation management methods and nutrient inputs, and improving the service functions of tropical agroecosystems.