Karst rocky desertification control through the conversion of cropland to economic forest is vital for vegetation recovery and the alleviation of distinct contradiction between ecological conservation and economic development. To evaluate the sustainability of orchard systems from the perspectives of ecosystem and economic services, we employed emergy analysis for the comprehensive and quantitative assessment of two orchard system types: (1) mango monoculture (MM) and macadamia monoculture (NM) and (2) mango Vicia angustifolia intercropping (MVI) and macadamia Desmodium intortum intercropping (NDI). In the past, these areas were converted from a maize field (MF) in the southwest karst area of China. Our results showed that, compared to the MF, the total emergy input in monoculture orchards (NM and NM) decreased by 8.99% and 35.25%, and the economic profit (EP) increased by 20,406.57 and 114,406.32 RMB·ha−1, respectively. However, the non-renewable environmental input (energy loss of soil, SOM reduction, and irrigation water) still accounted for 43.25% and 62.01% in the total emergy input. After conversion to orchard legume herb intercropping (MVI and NDI), purchased resource inputs accounted for 86.36% and 68.20% of the total emergy input. Orchard legume herb intercropping further increased the EP, while improving ecosystem services and providing the capability for groundwater recharge, soil conservation, and soil carbon sequestration. The intercropping orchards were relatively sustainable from the view of economic and ecosystem services (EISD > 3.18), due to lower environmental loading ratios (ELR < 1.15), higher emergy yield ratio (EYR > 0.89), and economic output/input ratio (O/I ratio > 2.41). The integrated pest management simulations indicated that, compared to intercropping systems, the renewable percent (R%) and emergy sustainability index (ESI) of the scenario simulations (MVI-O and NDI-O) increased by 17.61% and 10.51%, respectively. These results suggest that integrated pest management is an effective method to improve the short-term sustainability of the orchard system. Therefore, the management of intercropped legume herb within an orchard system is an effective way to achieve sustainable development.