As an important destination for China’s SOEs to invest overseas, EU’s merger control system has been the focus of academic and practical circles. Although in practice, the European Commission has almost approved the acquisition notification involving SOEs, in the process of identifying“single economy”, except confirming that all SOEs in the energy industry are regarded as a single economy; for other industries, the European Commission adopts an evasive attitude and the method of “worst case scenario”. Judged with this method, the conclusions are always against SOEs, which casts a shadow on the prospects for Chinese SOEs to invest in the EU. In addition, for those sensitive and strategic transactions, it may be subject to the Commission’s review based on public interest and other political factors. Therefore, the SOEs should be fully prepared with substantial evidence to prove that they have sufficient autonomy in business decision-making, and refute the query of unfair competition that may be suffered in the merger evaluation, to respond to the systematic discrimination of the European Commission against the merger transaction conducted by Chinese SOEs.