In light of escalating global climate change concerns and the pressing need to address industries with high carbon emissions and pollution, enhancing the preparation of phenol-formaldehyde epoxy resins has emerged as a critical research focus. This study seeks to fabricate waterborne phenol-formaldehyde epoxy resins with superior performance by investigating pivotal factors influencing their properties and refining preparation methods. Utilizing tetrabutylammonium bromide as a phase transfer catalyst, the phenol-formaldehyde epoxy resins are synthesized via a two-step alkalization process. Subsequent etherification reactions involve modifying the phenol-formaldehyde epoxy resins using cationic modifier diethanolamine (DEA) and anionic modifier sodium p-amino benzenesulfonate, resulting in waterborne phenol-formaldehyde epoxy resins. Subsequently, in situ synthesis is employed to produce nanoscale silica (SiO2) modified waterborne phenol-formaldehyde epoxy resins. The findings reveal that when the ratio of n1 to n2 falls within the range of 1/3.25 to 1/3, the emulsion displays a moderate particle size and maintains stable storage. Furthermore, an increase in DEA dosage leads to a particle size of less than 324 nm when the ratio of n1 to n2 exceeds 1/3, indicating stability. Moreover, optimal stability and prolonged storage lifespan are achieved when the nano SiO2 content is approximately 1.5%. This study contributes by synthesizing high-quality waterborne phenol-formaldehyde epoxy resin emulsions through optimized methods. The research findings offer a theoretical foundation for this domain and support the practical application of low-carbon and environmentally friendly concepts in the coatings industry.