A comparative analysis of the structure and function characteristics and ecological and economic benefits of different agroforestry models in a purple soil area in China was conducted. An agroforestry ecosystem composed of a pear forest and different crops planted under the local forest was taken as the research objective. The emergy analysis method was used to compare the emergy input and output of pear-rapeseed-maize system (model 1), pear-rapeseed-groundnut system (model 2), pear-wheat-maize system (model 3) and pear-wheat-sweet potato system (model 4). Results showed that the energy input structure in the four agroforestry models was similar. The investment of non-renewable emergy took a main proportion in the systems. The human labour emergy and the fertilizer emergy played dominant roles. Model 1 had the highest production efficiency, the most advantageous in price-competition, and the most powerful self-development. Model 4 had the lowest renewable resource utilization, the smallest environment load ratio and the biggest emergy sustainable indices. The net emergy yield ratio and emergy self-support ratio of model 2 were close to that of model 3. However, model 2 had a higher development potential because of its lower environment pressure. The science and technology level of the agroforestry ecosystem in the purple soil area was lower. The input of organic manure should be increased. Model 1 was the best model at present and model 4 was the most potential model for development.