The widely deployed passive optical network (PON) is a cost-effective way to create a front/backhaul carrier for ubiquitous wireless access connectivity. To hide the difference of frame formats and multiplexing methods, an orthogonal frequency division multiplexing access PON (OFDMA-PON) was proposed. In upstream transmission, multiple optical network units (ONUs) from the same segment or residential area can transmit data through a shared group of orthogonal low-bitrate subcarriers (SCs) during different time slots (TSs) within the entire transmitting period. In downstream transmission, the optical line terminal can send control signaling of reconfiguring ONUs’ parameters so that SCs can be reallocated among segments, thus sleeping segments with empty data load while ensuring service continuity. Though energy savings can be ensured for upstream data transmission by using existing solutions, only frequency and time domains are involved. It is meaningful for us to make the flexible and energy- efficient configuration of transmitting power and modulation level assigned for ONUs in terms of improving energy efficiency. In this paper, we investigate joint resource allocation for energy-efficient upstream data transmission in OFDMA-PONs, with the help of software-based ONU reconfiguration. We formulate the problem, and the upper bound of energy saving is also derived. To solve the problem in a short span of time, we propose a novel heuristic algorithm whose effectiveness has been demonstrated by extensive simulations.