Controlled-release fertilizers (CRF) use a controlled-release technology to enhance the nutrient use efficiency of crops. Many factors affect the release of nutrients from the waterborne polymer-coated CRF, but the effects of thermal post-treatments remain unclear. In this study, a waterborne polyacrylate-coated CRF was post-treated at different temperatures (30 °C, 60 °C, and 80 °C) and durations (2, 4, 8, 12, and 24 h) after being developed in the Wurster fluidized bed. To characterize the polyacrylate membrane, and hence to analyze the mechanism of nutrient release, Fourier transform mid-infrared spectroscopy, scanning electron microscopy, and atomic force microscopy were employed. The nutrient-release model of CRF post-treated at 30 °C was the inverse "L" curve, but an increased duration of the post-treatment had no effect. The nutrient-release model was "S" curve and nutrient-release period was enhanced at higher post-treatment temperatures, and increased post-treatment duration lengthened slowed nutrient release due to a more compact membrane and a smoother membrane surface as well as a promoted crosslinking action. CRF equipped with specified nutrient-release behaviors can be achieved by optimizing the thermal post-treatment parameters, which can contribute to the development and application of waterborne polymer-coated CRF and controlled-release technologies.