To achieve sustainable sugarcane cultivation in subtropical cropland of Okinawa, Japan, it is necessary to improve and maintain the soil fertility by organic matter application. In most islands of Okinawa, green manure (GM) application is commonly used to improve the soil organic matter content because of its cost effectiveness. In this study, we evaluated the effect of application of different GMs, i.e., Crotalaria juncea (CRO) and Sesbania cannabina (SES), on soil nutrient dynamics in relation to soil enzymes, which are a sensitive indicator of land management in a sugarcane field of Kitadaito, Okinawa. We evaluated the fluctuation of soil enzymes (dehydrogenase [DH], β-glucosidase [BG], and phosphomonoesterase [PHO]), soil nutrients (extractable carbon [Ext-C] and nitrogen [Ext-N], and available phosphorus [Avail-P]) with environmental conditions after GM application for seven months. We also measured the sugarcane growth parameters seven months after planting. Application of CRO and SES clearly increased the BG and PHO activities throughout the experimental period and increased the sugarcane number (ca. 11%-20%), but they did not increase the DH activity and soil nutrients (e.g., Ext-C and Avail-P). Application of CRO also increased Ext-N, but SES application had no clear effect, possibly because of the different GM quality and decomposition patterns. Thus, our results showed that CRO is the preferred GM species in terms of improvement of soil enzyme and nutrient conditions for GM-sugarcane cropping systems in Kitadaito.