Biomass energy, recognized as a “zero-carbon” energy, has gradually become a crucial approach to promoting the low-carbon transformation of agricultural rural industrial parks (ARIP). Meanwhile, modern agricultural facilities (MAF) can play a significant role in adjusting agricultural load. Therefore, this paper proposes a negative-carbon planning method for the ARIP integrated energy system (IES). Firstly, carbon activities occurring during the operation of ARIP are sorted out and modeled based on the life cycle assessment (LCA) method, especially modeling the “zero-carbon” and “negative-carbon” benefits of biomass energy. At the same time, the models of both agricultural irrigation systems and straw bundling direct combustion heating are constructed in the ARIP planning. Then, a negative-carbon planning model for ARIP IES is established with the goal of minimizing the annualized total cost, where carbon emission reduction is integrated into the optimization objectives through carbon trading. On this basis, a two-stage distributionally robust optimization (DRO) planning model is constructed, where a box-like set and comprehensive norm constraints are used to model the seasonal differences of agricultural industry loads and the uncertainty of probability distribution in photovoltaic (PV) scenarios. Especially, a box set with adjustable uncertainty coefficients is introduced to simulate fluctuations of output in PV scenario. Finally, the CPLEX solver is used to solve the planning model. verify the effectiveness of the proposed planning method in enhancing the economic and environmental effects of ARIP. Results indicate that the proposed planning model can reduce the total cost by 49.584 × 104 $. Besides, the annual carbon emissions can be reduced from 37533.98 t CO2-eq to −15834.5 t CO2-eq. Especially, the carbon sequestration effect of biochar is the key link in achieving “negative carbon” in ARIP.