The intensification and industrialization of agricultural production leads to more and more serious separation of crop and livestock, which causes serious contradiction between livestock excrement and environment, and major challenges for agricultural sustainable development. Here, we quantitatively investigated the spatial pattern and evolutionary trend of the sustainable development index (ESI) of the crop-livestock system using the emergy analysis and the input/output data in Shandong Province (1999-2015). The results showed that the sustainability of the crop-livestock system in Shandong Province decreased from 1999 to 2015 by 22.0%. The net emergy yield ratio (EYR), environmental load ratio (ELR), and the benefits of unit economic inputs significantly increased. The environmental pressure from the crop and livestock production increased obviously, which was closely related to the increase of industrial resources input including electricity, compound fertilizer, and agricultural machinery. There were differences in the sustainable development level of the crop-livestock system among administrative prefectures in Shandong Province. The ESI level of crop-livestock system in most regions was relatively high, while that in the coastal regions (e.g., Weihai, Yantai) and industrial region (e.g., Zibo) was relatively low. The trends of the sustainable development of crop-livestock system varied in different cities. The sustainability of central and southern Shandong was decreasing, while that of northern Shandong was increasing year by year. In 2015, the ESI of the expected crop-livestock system (100% livestock manure replaced fertilizer) could reach 8.4, which was 2.6 times of that of the current crop-livestock system (30% livestock manure replaced fertilizer).