To explore an effective method for comprehensive assessment of the effect of collaborative treatment on environmental pollution in the Yangtze River Delta urban agglomeration, this paper selects four categories of 22 assessment indicators: the driving force of collaborative treatment, the pressure of collaborative treatment, the synergy degree of collaborative treatment, and the result of collaborative treatment to construct an assessment indicator system. Based on the technical treatment of the assessment indicators, the absolute niche suitability (ANS) model, the relative niche suitability (RNS) model and the spatial niche suitability (SNS) model were constructed, and the research on the effect of environmental pollution treatment in the Yangtze River Delta was applied. The assessment results were discussed in depth to verify the effectiveness of the assessment models. The study found that the spatial niche suitability assessment model has the best assessment effect. The assessment result obtained by the SNS model increased from 0.7989 in 2012 to 0.9186 in 2020, the effect of environmental pollution collaborative treatment increased from Level III in 2012 to Level I in 2020. The research results of this paper provide theoretical support for guiding the collaborative treatment of environmental pollution in the Yangtze River Delta urban agglomeration and for local governments to formulate corresponding environmental pollution collaborative treatment polices.