Flexible production centring on machines or job-shops is necessary to meet the current trend of production and sales. By studying the energy consumption of production logistics, it is possible to minimize energy consumption and carbon emissions of the production process, without sacrificing production efficiency. The existing studies all try to optimize the logistics distribution. None of them attempt to optimize both production and logistics distribution parameters, and low carbon emission indices. Therefore, this paper explores the multi-objective optimization and carbon efficiency evaluation of flexible production logistics under low carbon constraint. Specifically, the constraint order between production logistics time, logistics quality, logistics cost, and low-carbon degree was determined, and the expressions of four linear programming models were given. Moreover, the carbon efficiency optimization of flexible production logistics was redefined, and a mathematical model was developed for the carbon efficiency optimization problem, which simultaneously optimizes carbon emissions and production indices. The proposed model was proved scientific through experiments.