This article describes the new Earth system model (ESM), the Model for Interdisciplinary Research on Climate, Earth System version 2 for Long-term simulations (MIROC-ES2L), using a state-of-the-art climate model as the physical core. This model embeds a terrestrial biogeochemical component with explicit carbon-nitrogen interaction to account for soil nutrient control on plant growth and the land carbon sink. The model's ocean biogeochemical component is largely updated to simulate the biogeochemical cycles of carbon, nitrogen, phosphorus, iron, and oxygen such that oceanic primary productivity can be controlled by multiple nutrient limitations. The ocean nitrogen cycle is coupled with the land component via river discharge processes, and external inputs of iron from pyrogenic and lithogenic sources are considered. Comparison of a historical simulation with observation studies showed that the model could reproduce the transient global climate change and carbon cycle as well as the observed large-scale spatial patterns of the land carbon cycle and upper-ocean biogeochemistry. The model demonstrated historical human perturbation of the nitrogen cycle through land use and agriculture and simulated the resultant impact on the terrestrial carbon cycle. Sensitivity analyses under preindustrial conditions revealed that the simulated ocean biogeochemistry could be altered regionally (and substantially) by nutrient input from the atmosphere and rivers. Based on an idealized experiment in which CO2 was prescribed to increase at a rate of 1% yr(-1), the transient climate response (TCR) is estimated to be 1.5 K, i.e., approximately 70% of that from our previous ESM used in the Coupled Model Intercomparison Project Phase 5 (CMIP5). The cumulative airborne fraction (AF) is also reduced by 15% because of the intensified land carbon sink, which results in an airborne fraction close to the multimodel mean of the CMIP5 ESMs. The transient climate response to cumulative carbon emissions (TCRE) is 1.3KEgC(-1), i.e., slightly smaller than the average of the CMIP5 ESMs, which suggests that "optimistic" future climate projections will be made by the model. This model and the simulation results contribute to CMIP6. The MIROC-ES2L could further improve our understanding of climate-biogeochemical interaction mechanisms, projections of future environmental changes, and exploration of our future options regarding sustainable development by evolving the processes of climate, biogeochemistry, and human activities in a holistic and interactive manner.