The reflooding phase, a crucial recovery process after a loss of coolant accident (LOCA) in reactors, involves cooling overheated fuel rods with subcooled water. Its complex nature, notably in its flow regime and heat transfer, makes prediction challenging, resulting in high uncertainty and computation cost. In this study, we utilized the data assimilation (DA) technique to enhance the prediction of reflooding phenomena and subsequently deployed machine learning models to predict the accuracy of the safety and performance analysis code (SPACE) simulation. To generate the dataset for the machine learning model, we employed the sampling method for highly nonlinear system uncertainty analysis (STARU), providing a high-quality dataset for a complex problem such as a reflooding simulation. In this dataset, the physical models were assimilated under their selected uncertainty bands and utilized the effective sampling approach of STARU, generating the high-quality output and efficient enhancement of SPACE predictions. Consequently, the implemented machine learning model can be used to enhance model development and uncertainty quantification (UQ) analysis using the system code.