Abstract: Over the past few decades, the intensive use of chemicals in agricultural production in China has led to serious environmental and food safety problems, triggering a series of public health incidents and greatly undermining consumer confidence in traditional food. Due to food safety concerns, consumers in developed as well as developing countries such as China have been paying increasing attention to emerging ecological agricultural products (EEAPs) produced in environmentally conscious way. In the consumer market, guiding consumers to pay reasonable fees for EEAPs is not only conducive to promote the cultivation and development of the EEAPs market but also has important practical significance for improving the health of residents and ensuring environmental protection. Using green manure-rice (GMR) as an example, based on survey data from 974 consumers in Changsha, Wuhan, Nanchang, and Hefei in South China, this study first used the contingent valuation method (CVM) to evaluate consumers’ premium payment level for GMR. Then, the Heckman two-stage model was used to explore the mechanism of influence of consumer motivation and consumption habits on consumers’ willingness to pay (WTP) and to empirically test the moderating effect of external environmental cognition on the process by which consumer motivation affects WTP. The study showed that the average premium paid by consumers for GMR was 61.69%, the premium value calculated from premium ratio and conventional rice price was 3.27 ¥∙kg⁻¹, and the actual price consumers willing to pay for GMR was 8.57 ¥∙kg⁻¹. External environment cognition had the greatest influence on consumers’ WTP, and safety motivation and environmental motivation also had a significant positive influence on consumers’ WTP. Positive external environment cognition significantly improved consumers’ WTP by strengthening their safety and environmental motivation. In addition, young women with higher education level, children, and consumers with higher household income and pursuit of quality of life were more willing to pay a higher premium for GMR. Accordingly, this study had the following policy implications. First, a scientific pricing mechanism for green manure rice should be established as soon as possible to ensure improved returns for producers that are acceptable to consumers. Second, enhancing consumers’ cognition of the external environment is the key to encouraging them to pay a premium for GMR. The improvement of consumers’ comprehensive cognition of the external environment and the risks to the natural environment can enhance their perception of the value of GMR, thus increasing their WTP. Third, paying attention to consumers’ motivation contributes to a deeper understanding of the process and mechanism of premium payment behavior, which is conducive to shaping stable consumption preferences, thus improving the sustainability of consumers’ premium payments for GMR.