To explore the effects of different inoculation methods on the flavor compounds of kiwifruit-apple compound fruit wine fermented at low temperature, solid phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) was used to analyze the mixed fruit wine fermented by Angel yeast SY and Hanseniaspora uvarum CICC 193162 with five different inoculation methods (single inoculation, simultaneous mixed inoculation, and sequential mixed inoculation). A total of 74 aroma components were detected, comprising 15 alcohols, 35 esters, 6 acids, 10 terpenes and phenols, and 8 ketones and aldehydes. The acid and alcohol contents were lowest in wine inoculated with H. uvarum, followed by wine inoculated with Angel yeast SY (JGHUSY4). The types and contents of esters in fruit wine fermented by mixed inoculation were higher than those by Angel yeast SY alone. The JGHUSY4 wine has the highest ester content, as well as the types, quantity, and mass concentration (45.986 mg•mL-1) of volatile flavor compounds were also highest. Eight types of organic acids were detected using high-performance liquid chromatography in the five types of fruit wines produced by different fermentation methods. The results showed that the acetic acid content decreased, whereas lactic acid and quinic acid contents increased during mixed fermentation, indicating that mixed fermentation had a positive effect on fruit wine, and the quality of JGHUSY4 wine was the best. Therefore, the fruit wine obtained by mixed fermentation was superior to that obtained by inoculation with Angel yeast SY or H. uvarum CICC 193162 alone, with the best results achieved when H. uvarum CICC 193162 was inoculated 72 h before Angel yeast SY. This study provides a theoretical foundation for optimizing the low-temperature fermentation process and regulating the flavor of kiwifruit-apple compound wine.