This paper considers multi-cell decode-and-forward (DF) relay-aided orthogonal frequency division multi-access (OFDMA) downlink systems, in which all sources and relays are coordinated by a central controller for resource allocation (RA). The improved subcarrier pair-based opportunistic DF relaying protocol proposed and studied in the IEEE International Conference on Communications, Beijing, 3795–3800, 2008 and IEEE Trans. Signal Process. 61:2512–2524, 2013 is applied. This protocol has a high spectrum efficiency (HSE) in the sense that all unpaired subcarriers are utilized for data transmission during the second time slot (TS). In particular, the sum (over all cells and all destinations) rate maximized problem with a total power constraint in each cell+ is formulated. To solve this problem, an iterative RA algorithm is proposed to optimize mode selection (decision whether the relay should help or not), subcarrier assignment and pairing (MSSAP) and power allocation (PA) in an alternate way. As for the MSSAP stage of each iteration, the formulated problem is decoupled into subproblems with the tentative PA results. Each subproblem can be easily solved by using the optimal results of a linear assignment problem (LAP), which is then solved by the Hungarian Algorithm in polynomial time. As for the PA stage of each iteration, an algorithm based on single-condensation and geometric programming (SCGP) is proposed to optimize PA in polynomial time with the tentative MSSAP results. The proposed algorithm is coordinate ascent (CA)-based and therefore can reach a local optimum in polynomial time. Finally, the convergence and effectiveness of the proposed algorithm, the impact of relay position and total power on the system performance, and the benefits of using subcarrier pairing (SP) and the HSE protocol are illustrated through numerical experiments.