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Domain adaptation techniques using deep neural networks have been mainly used to solve the distribution shift problem in homogeneous domains where data usually share similar feature spaces and have the same dimensionalities. Nevertheless, real world applications often deal with heterogeneous domains that come from completely different feature spaces with different dimensionalities. In our remote sensing application, two remote sensing datasets collected by an active sensor and a passive one are heterogeneous. In particular, CALIOP actively measures each atmospheric column. In this study, 25 measured variables/features that are sensitive to cloud phase are used and they are fully labeled. VIIRS is an imaging radiometer, which collects radiometric measurements of the surface and atmosphere in the visible and infrared bands. Recent studies have shown that passive sensors may have difficulties in prediction cloud/aerosol types in complicated atmospheres (e.g., overlapping cloud and aerosol layers, cloud over snow/ice surface, etc.). To overcome the challenge of the cloud property retrieval in passive sensor, we develop a novel VAE based approach to learn domain invariant representation that capture the spatial pattern from multiple satellite remote sensing data (VDAM), to build a domain invariant cloud property retrieval method to accurately classify different cloud types (labels) in the passive sensing dataset. We further exploit the weight based alignment method on the label space to learn a powerful domain adaptation technique that is pertinent to the remote sensing application. Experiments demonstrate our method outperforms other state-of-the-art machine learning methods and achieves higher accuracy in cloud property retrieval in the passive satellite dataset.