Root-knot nematodes (RKNs) are the most economically damaging plant-parasitic nematodes globally. Xinjiang, encompassing one-sixth of China’s landmass, currently lacks comprehensive data regarding the occurrence, distribution, and genetic variation of RKNs infecting vegetables within its borders. Hence, identifying RKNs species and genetic diversity is crucial for devising comprehensive management strategies. Between 2021 and 2023, we present a survey of 130 samples, collected from 86 counties across 14 cities in Xinjiang, China, aiming to comprehensively understand the occurrence, distribution, damage, and species of vegetable RKNs. The results indicated that 57 out of 130 samples collected from the regions of Hami, Tulufan, Ili, Bayingol, Hotan, Aksu, Kashgar, and Kizilsu in Xinjiang were infected by RKNs, suggesting an expansion of RKN disease in the vegetable-producing regions of Xinjiang. The infected vegetable roots were found to harbor Meloidogyne incognita and M. hapla, with M. incognita being the most prevalent species. A phylogenetic analysis of the COI region revealed significant evolutionary divergence between M. incognita populations from Xinjiang and those from southeastern provinces. Haplotype analysis of the COI gene revealed that M. incognita populations are categorized into three major lineages: Asia, Europe, and a combined lineage encompassing both America and Africa. Notable gene flow patterns were observed among M. incognita populations, with significant migrations from Europe and America to Asia, specifically from the southeastern China towards Xinjiang. This study’s findings indicate a consistent increase in the detrimental effects of vegetables production caused by RKNs in Xinjiang. Implementing effective prevention and control measures is crucial to mitigate the spread of RKNs.