Understanding changes in nitrogen (N) and phosphorus (P) flows with the changes of crop-livestock systems is critical for sustainable agricultural development but has received little attention. This study presents a case study to estimate N and P flow changes in crop-livestock systems, of the dramatic agricultural transformation of Pinghe, an emerging county in Southeast China. The main nutrient inputs and outputs in the crop systems were fertilizer and soil accumulation, respectively. In the livestock system, the main nutrient inputs and outputs were imported feed and recycled manure, respectively. From 1985 to 2015, the total N and P inputs into Pinghe’s crop-livestock system increased from 11.0 and 1.2 Gg (Gg = 10⁹ g) to 53.0 and 11.9 Gg, respectively. N and P use efficiency of the crop systems decreased from 24 and 42% to 10 and 6%, respectively; those in the livestock systems increased from 13 and 6% to 16 and 7%, respectively. The overall N and P use efficiency of the crop-livestock system decreased from 32 and 50% to 11 and 6%, respectively. The sharp increase in nutrient input and decrease in internal nutrient recycling are the main reasons for the decrease in system nutrient use efficiency. Scenario analyses indicated that there are large options for improving nutrient use efficiency and decreasing nutrient losses. We recommend a strong control of nutrient inputs, a tight coupling of crop and livestock production systems with effective manure recycling, and buffer areas between agricultural land and vulnerable water bodies, and with erosion control in hilly areas.