FY‐3E plays a vital role in the meteorological global earth observing system. Precipitable water vapor (PWV) is an essential parameter for the water cycle and global climate change. Here, we carry out the PWV retrieval using the MERSI‐LL sensor onboard the FY‐3E satellite for the first time. The retrieval accuracy under different cloudage conditions is validated by the extra PWV from ground‐based GNSS and spaceborne occultation. For the results against ground‐based GNSS, the total accuracy shows an RMSE of 2.69–3.36 mm as the clouds increase, and correlation coefficients higher than 0.95. The spatial accuracy distribution indicates that inland stations have higher accuracy than the coast and island stations. As for the results against spaceborne occultation, the verification accuracy varies with the spatial pairing distance, showing poor accuracy in the low latitude area. This study can provide an essential reference for the community to understand the current water vapor inversion performance of MERSI‐LL.