Heritage conservation is an important recurring research theme on agricultural heritage systems. Improving the income of farmers from agriculture is regarded as an effective conservation approach. This study examined how the improved rice-fish-duck coculture (IRFDC) promotes the protection of the Honghe Hani Rice Terraced System (HHRTS) by keeping farmers farming in their hometowns. A semi-structural interview and a questionnaire survey were used to collect data on agricultural input–outputs and household employment in HHRTS. As a result, a fairly large proportion of HHRTS rice terraces were used for the hybrid rice monoculture (HRM) with chemical inputs, and most of these rice terraces were wasted for half a year on account of being left unused; the IRFDC requires considerable time input for farming and breeding, but barely needs any chemical inputs. IRFDC entails a higher cost than HRM, but also has a higher return than HRM. Driving a family to do full-time farming requires extra more than 0.71 ha rice terraces for IRFDC. In conclusion, Globally Important Agricultural Heritage Systems (GIAHSs) can be used for protecting terraces from abandonment and destruction by improving agricultural economic benefits for farmers. At present, a shortage of laborers in HHRTS sites is false. Agricultural heritage sites do not actual need so many people if peasant households can do large-scale farming.