Nonstoichiometry and Na incorporation are designed to attain controllable impurity phases Li4P2O7 and Li3PO4 in LiFePO4. The effects of Li4P2O7 and Li3PO4 on structure and electrochemical performance have been investigated. Both Li4P2O7 and Li3PO4 impurities are observed in (Fe, P)-deficient LiFe0.9P0.95O4−δ . With Na+ incorporation, Li4P2O7 phase disappears while Li3PO4 content increases. Proved by X-ray photoelectron spectroscopy, nonstoichiometry and Na-incorporation do not change the chemical state of Fe(II). Our experiments indicate that Li4P2O7 and Li3PO4 show different effects on the electrochemical performance. Li4P2O7 leads to degradation of cyclability, whereas a small amount of Li3PO4 is beneficial for the improvement in capacity and rate capability. The 1% Na-doped LiFe0.9P0.95O4−δ composite exhibits the best electrochemical performance. We ascribe the improvement to the structural stabilization caused by the existence of Li3PO4.