The actual operating experience of XingAn high voltage direct current (HVDC) system in China indicates that in addition to the characteristic harmonics, the negative impact of low-order non-characteristic harmonics in line commutated converter (LCC) based HVDC is also prominent. Based on the actual operation data of XingAn HVDC system, this paper investigates the generation mechanism of low-order non-characteristic harmonics and verifies the analysis resorts to the simulation model in PSCAD/EMTDC. Furtherly, according to the IEEE Std C57.91-2011, this paper proposes an improved hot-spot temperature calculation method considering the harmonics, and the impact of low-order non-characteristic harmonics on the converter transformer is thereby revealed. Some practical suggestions are provided in the end to mitigate the effect of these low-order non-characteristic harmonics.