Agricultural production in Minqin Oasis, China, is commonly categorized as intensive crop production (ICP), integrated crop-livestock production (ICLP), intensive livestock production (confined feeding) (IFLP), and extensive livestock production (grazing) (EGLP). The objectives of the present study were to use a life cycle assessment technique to evaluate on-farm energy balances and greenhouse gas (GHG) emissions of agricultural production, and to compare the differences among the four systems. Data used in the present study were collected from published literature and face-to face questionnaires from 529 farms in eight towns (two towns per production system) within Minqin county. The ANOVA of averaged data from 2014 to 2015 indicated that the net energy ratio (Output/Input) for the EGLP system was significantly higher than that for any other system ( < 0.01), whereas the difference among other three systems were not significant. The EGLP system generated lower CO-eq emissions per hectare of farmland than other systems ( < 0.01). Relating carbon economic efficiency to market values (US$) of agricultural products, indicated that the carbon economic efficiency (US$/kg CO-eq) of the IFLP system was significantly greater than that of other systems ( < 0.01). The major GHG emission sources varied across the systems, that is, soil respiration is the dominant source in EGLP, while the main sources in IFLP are enteric methane and manure management; in ICLP major sources are enteric methane, soil respiration and fertilizer; and in ICP are soil respiration and fertilizer. The structural equation modelling analysis showed that livestock category was strongly linked to net income. The direct effects and total effects of water use efficiency, via its positive influence on energy balances and GHG emissions were much stronger than those of other dependent variables. The study provides important benchmark information to help develop sustainable agricultural production systems on energy balances and GHG emissions in northwestern China.