Abstract. This study developed a new Model for Interdisciplinary Research on Climate, Earth System version2 for Long-term simulations (MIROC-ES2L) Earth system model (ESM) 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 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 the model could reproduce reasonable historical changes in climate, the carbon cycle, and other biogeochemical variables together with reasonable spatial patterns of distribution of the present-day condition. The model demonstrated historical human perturbation of the nitrogen cycle through land use and agriculture, and it simulated the resultant impact on the terrestrial carbon cycle. Sensitivity analyses in preindustrial conditions revealed modeled ocean biogeochemistry could be changed regionally (but substantially) by nutrient inputs from the atmosphere and rivers. Through an idealized experiment of a 1 %CO2 increase scenario, we found the transient climate response (TCR) in the model is 1.5 K, i.e., approximately 70 % that of our previous model. The cumulative airborne fraction (AF) is also reduced by 15 % because of the intensified land carbon sink, resulting in an AF close to the multimodel mean of the Coupled Model Intercomparison Project Phase 5 (CMIP5) ESMs. The transient climate response to cumulative carbon emission (TCRE) is 1.3 K EgC−1, i.e., slightly smaller than the average of the CMIP5 ESMs, suggesting optimistic model performance in future climate projections. This model and the simulation results are contributing to the Coupled Model Intercomparison Project Phase 6 (CMIP6). The ESM could help further 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.