Accurate and timely modeling of labor migration is crucial for various urban governance and commercial tasks, such as local policy-making and business site selection. However, existing studies on labor migration largely rely on limited survey data with statistical methods, which fail to deliver timely and fine-grained insights for time-varying regional trends. To this end, we propose a deep learning-based spatial-temporal labor migration analysis framework, DHG-SIL, by leveraging large-scale job query data. Specifically, we first acquire labor migration intention as a proxy of labor migration via job queries from one of the world’s largest search engines. Then, a discrepant homophily co-preserved graph convolutional network and an interpretable temporal module are respectively proposed to capture cross-city and sequential labor migration dependencies. Besides, we introduce four interpretable variables to quantify city migration properties, which are co-optimized with city representations via tailor-designed contrastive losses. Extensive experiments on three real-world datasets demonstrate the superiority of our DHG-SIL. Notably, DHG-SIL has been deployed as a core component of a cooperative partner’s intelligent human resource system, supporting a series of city talent attraction reports.