Aiming at the resource allocation problem of a non-orthogonal multiple access (NOMA) system, a fairness index based on sample variance of users’ transmission rates is proposed, which has a fixed range and high sensitivity. Based on the proposed fairness index, the fairness-constrained power allocation problem in NOMA system is studied; the problem is decoupled into the intra cluster power allocation problem and the inter cluster power allocation problem. The nonconvex optimization problem is solved by the continuous convex approximation (SCA) method, and an intra and inter cluster power iterative allocation algorithm with fairness constrained is proposed to maximize the total throughput. Simulation results show that the proposed algorithm can take into account intra cluster, inter cluster, and system fairness, and maximize the system throughput on the premise of fairness.