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Abstract Understanding and forecasting Tropical Pacific Decadal‐scale Variability (TPDV) strongly rely on climate model simulations. Using a Linear Inverse Modeling (LIM) diagnostic approach, we reveal Coupled Model Intercomparison Project Phase 6 models have significant challenges in reproducing the spatial structure and dominant mechanisms of TPDV. Specifically, while the models' ensemble mean pattern of TPDV resembles that of observations, the spread across models is very large and most models show significant differences from observations. In observations, removing the coupling between extratropics and tropics reduces TPDV by ∼60%–70%, and removing the tropical thermocline variability makes the central tropical Pacific a key center of action for TPDV and El Niño Southern Oscillation variability. These characteristics are only confirmed in a subset of models. Differences between observations and simulations are outside the range of natural internal TPDV noise and pose important questions regarding our ability to model the impacts of natural internal low‐frequency variability superimposed on long‐term climate change. 

Abstract Assessing uncertainty in future climate projections requires understanding both internal climate variability and external forcing. For this reason, single‐model initial condition large ensembles (SMILEs) run with Earth System Models (ESMs) have recently become popular. Here we present a new 20‐member SMILE with the Energy Exascale Earth System Model version 1 (E3SMv1‐LE), which uses a “macro” initialization strategy choosing coupled atmosphere/ocean states based on inter‐basin contrasts in ocean heat content (OHC). The E3SMv1‐LE simulates tropical climate variability well, albeit with a muted warming trend over the twentieth century due to overly strong aerosol forcing. The E3SMv1‐LE's initial climate spread is comparable to other (larger) SMILEs, suggesting that maximizing inter‐basin ocean heat contrasts may be an efficient method of generating ensemble spread. We also compare different ensemble spread across multiple SMILEs, using surface air temperature and OHC. The Community Earth system Model version 1, the only ensemble which utilizes a “micro” initialization approach perturbing only atmospheric initial conditions, yields lower spread in the first ∼30 years. The E3SMv1‐LE exhibits a relatively large spread, with some evidence for anthropogenic forcing influencing spread in the late twentieth century. However, systematic effects of differing “macro” initialization strategies are difficult to detect, possibly resulting from differing model physics or responses to external forcing. Notably, the method of standardizing results affects ensemble spread: control simulations for most models have either large background trends or multi‐centennial variability in OHC. This spurious disequlibrium behavior is a substantial roadblock to understanding both internal climate variability and its response to forcing.