As Connected and Automated Vehicles (CAVs) gradually occupy more market share, the mixed traffic flow composed of MVs and CAVs will exist for a long time. This paper mainly explores the impact of CAV platoon management and control mode degradation on the fundamental diagram, and further studies how they affect fuel consumption and pollutant emissions. First, in terms of platoon management, the mixed traffic flow configurations and distribution characteristics of four types of vehicles were proposed. Second, numerical analyses were conducted, and a fundamental diagram considering CAV platoons and degradation of the Cooperative Adaptive Cruise Control (CACC) system was proposed. To validate this fundamental diagram, the Intelligent Driver Model (IDM) and the Connected and Automated Vehicle (CAV) and CACC models proposed by the PATH lab were applied for simulations. Third, the influence of CAV platoons on the traffic environment was explored via micro simulations as well. Conclusions were drawn from the results of the simulations: The mixed traffic can obtain significant capacity gain due to the existence of CAV platoons, especially with high Market Penetration Rate (MPR). Moreover, capacity break-downs occurred in the diagram due to the adjustment of information flow topology, and the break-downs were more prominent with higher MPR. Additionally, CAV platoons can significantly reduce fuel consumption and emissions by 34.7% and 41.4% respectively. The first degradation raises fuel consumption and emissions by 44.5% and 60.1%, while the second one by 12.0% and 16.1%, with the initial vehicle speed set at 33 m/s and MPR set at 1.0. Finally, according to the sensitivity analysis, an optimal platoon size of 5 vehicles was suggested for CAV platoon management.