This paper provides a literature review of freight transportation service procurement and investigates the challenges and opportunities regarding transportation organization and procurement mechanism design in the context of E-commerce. A total of 78 articles published in academic journals between 1998 and 2017 were reviewed. A framework comprising seven classification criteria is proposed to analyze the articles. The results reveal that new business environments challenge the efficiency and effectiveness of the current leading procurement mechanisms. This work also identifies the trends and gaps from the viewpoints of practitioners and researchers and describes future prospects in new freight transportation markets and organizations.