To investigate the crystal structure and electrochemical performance of samples synthesized under different microwave solid-state synthesis condition, a series of Li3V2(PO4)3 samples has been synthesized at five different temperatures for 3–5min and at 750°C for various time. The as-synthesized Li3V2(PO4)3 samples are characterized and studied by ICP-AES analysis, X-ray diffraction (XRD), Rietveld analysis, scanning and transmission electron microcopy (SEM and TEM). At relatively lower temperature (650°C) and very short reaction time (3min), pure phase of Li3V2(PO4)3 could be synthesized in microwave irradiation field. The crystal structure and Li atomic fractional coordinate present a significant deviation upon the change of microwave irradiation temperature and time. Relatively, the diffusion ability of lithium cations and the electrochemical performance are affected. Under the proper reaction temperature and time, the carbon-free samples MW750C5m and MW850C3m show the best specific discharge capacity 126.4 and 132mAhg−1 at the voltage range of 3.0–4.3V, near the reversible cycling of two lithium ions per Li3V2(PO4)3 formula unit (133mAhg−1). At the voltage range of 3–4.8V, the sample MW750C5m presents the best initial specific charge capacity of 197mAhg−1, equivalent to the reversible cycling of three lithium ions per Li3V2(PO4)3 formula unit (197mAhg−1). The initial discharge capacity, the samples MW750C5m and MW850C3m present high specific discharge capacity 183.4 and 175.7mAhg−1, respectively. The relationship among microwave irradiation condition, crystal structure, lithium atomic fractional coordinates and the electrochemical performance have been discussed in detail.