Brain lesion mapping studies have provided the strongest evidence regarding the neural basis of cognition. However, it remained a problem to identify symptom-specific brain networks accounting for observed clinical and neuroanatomical heterogeneity. Independent component analysis (ICA) is a statistical method that decomposes mixed signals into multiple independent components. We aimed to solve this issue by proposing an independent component-based lesion mapping (ICLM) method to identify the language network in patients with moderate to severe post-stroke aphasia. Lesions were first extracted from 49 patients with post-stroke aphasia as masks applied to fMRI data in a cohort of healthy participants to calculate the functional connectivity (FC) within the masks and non-mask brain voxels. ICA was further performed on a reformatted FC matrix to extract multiple independent networks. Specifically, we found that one of the lesion-related independent components (ICs) highly resembled classical language networks. Moreover, the damaged level within the language-related lesioned network is strongly associated with language deficits, including aphasia quotient, naming, and auditory comprehension scores. In comparison, none of the other two traditional lesion mapping methods found any regions responsible for language dysfunction. The language-related lesioned network extracted with the ICLM method showed high specificity in detecting aphasia symptoms compared with the performance of resting ICs and classical language networks. In total, we detected a precise language network in patients with aphasia and proved its efficiency in the relationship with language symptoms. In general, our ICLM could successfully identify multiple lesion-related networks from complicated brain diseases, and be used as an effective tool to study brain-behavior relationships and provide potential biomarkers of particular clinical behavioral deficits.