Our longest, stable record of cloud-top pressure (CTP) and cloud-top height (CTH) are derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Multi-Angle Imaging Spectroradiometer (MISR) on Terra. Because of single cloud-layer assumptions in their standard algorithms, they provide only single CTP/CTH retrievals in multi-layered situations. In the predominant multi-layered regime of thin cirrus over low clouds, MODIS significantly overestimates cirrus CTP and emissivity, while MISR accurately retrieves low-cloud CTH. Utilizing these complementary capabilities, we develop a retrieval algorithm for accurately determining both-layer CTP and cirrus emissivity for such 2-layered clouds, by applying the MISR low-cloud CTH as a boundary condition to a modified MODIS CO2-slicing retrieval. We evaluate our 2-layered retrievals against collocated Cloud-Aerosol Transport System (CATS) lidar observations. Relative to CATS, the mean bias of the upper cloud CTP and emissivity are reduced by ∼90% and ∼75% respectively in the new technique, compared to standard MODIS products. We develop an error model for the 2-layered retrieval accounting for systematic and random errors. We find up to 87% of all residuals lie within modeled 95% confidence intervals, indicating a near-closure of error budget. This reduction in error leads to a reduction in modeled atmospheric longwave radiative flux biases ranging between 5 and 40 W m −2, depending on the position and optical properties of the layers. Given this large radiative impact, we recommend that the pixel-level 2-layered MODIS + MISR fusion algorithm be applied over the entire MISR swath for the 22-year Terra record, leading to a first-of-its-kind 2-layered cloud climatology from Terra's morning orbit. Plain Language Summary Our longest climate-quality record of global cloud-top heights (CTH) comes from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Multi-Angle Imaging Spectroradiometer (MISR) on the Terra satellite. These sensors assume a single cloud-layer in retrieving CTH, even though ∼30% of global cloud cover is multi-layered. Multi-layered clouds predominantly consist of thin ice clouds over low clouds. Under such conditions, MISR accurately retrieves low-cloud CTH, while MODIS systematically underestimates upper-cloud-layer CTH. Here, we have developed a 2-layered MODIS + MISR fusion CTH retrieval by using MISR's accurate low-cloud CTH as an input to a modified MODIS algorithm. This algorithm combines the complementary capabilities of MISR and MODIS in distinguishing higher and lower clouds and estimates both-layer cloud heights and high-cloud emissivity. Through comparisons against coincident Cloud-Aerosol Transport System lidar observations, we find that the new algorithm improves the accuracies in retrieved CTH and cloud emissivities by ∼75% over standard MODIS products. We further demonstrate significant improvements in estimates of simulated atmospheric longwave radiation from our implementation. Owing to its large radiative impact, we suggest that the pixel-level fusion algorithm be applied to all 22 years of Terra record to facilitate public dissemination of the first 2-layered cloud record from its morning orbit.