Shale gas is the key focus of energy development in the twenty-first century. The physical characteristics of shale gas include microscale effect, mixed gas effect (MGE), and real gas effect (RGE). In addition, the geometry size of natural microscale fracture (NMF) should be modeled. However, to the best of our knowledge, these factors are not totally considered in existing models. In this paper, a new model is presented for simulating gas mixture (GM) seepage in NMF with consideration of MGE, RGE and equivalent radius (ER). The simulated results show that: (a) All seepage mechanisms co-exist during the seepage process no matter how the geometry changes. (b) When the GM is very thin or the pressure is low, the transient flow (TF) line is closer to the Knudsen diffusion (KD) line, while when the GM is dense or the pressure is high, the TF line is closer to the SF line. (c) When the geometry size is reduced, the RGE becomes more obvious. The effect of SL on TF is weakened, while the effect of KD on TF is strengthened. (d) The weighting coefficient (WC) of slippage flow (SF) decreases when the geometry size of NMF is reduced; the WC of KD increases when the geometry size of NMF is reduced. In addition, compared with ideal GM, the RGE leads to a lower WC of SF, and the RGE leads to a higher WC of KD. (e) There exists a turning point (TP) for MTR with the increasing of pressure. (f) Below the TP, the MTR increases with pressure, while above the TP, the MTR decreases with pressure. This study presents a useful analytical model for engineers to estimate the transport capacity of GM in NMF and also provides basic equations for software companies to develop gas reservoir numerical simulation software.