How to quantitatively measure the eco-environment loss caused by industrial solid waste (ISW) and how to determine the ecological compensation criterion reasonably have been recognised as a problem of improving the environment performance. To solve this challenge, this study uses emergy theory to calculate emergy loss of ISW with different treatments for quantitatively measuring the eco-environment loss. Then the ecological compensation criterion of ISW is established to compensate for the loss based on sustainability. The pollution tax of ISW is introduced to balance the pollution-control effectiveness and the eco-environment loss, further the government fines for the discarded ISW can be determined. Finally, the case study is performed to analyse and calculate the phosphogypsum emission as the ISW in a city. The results show that the ecological compensation criterion is 37.4 CNY/ton, and its pollution tax should be determined as 44.9 CNY/ton. Therefore, the government fines should be no less than 350.5 CNY/ton for the discard phosphogypsum. Besides, the phosphogypsum pollution tax (30 CNY/ton, National standard) is not satisfied with the pollution of the city's ecologic environment losses. This study gives an effective reference standard for the government decision makers in pollution tax of the industrial waste.