With the increasing application scenarios and detection needs of high‐field asymmetric waveform ion mobility spectrometry (FAIMS) analysis, deep learning–assisted spectral analysis has become an important method to improve the analytical effect and work efficiency. However, a single model has limitations in generalizing to different types of tasks, and a model trained from one batch of spectral data is difficult to achieve good results on another task with large differences. To address this problem, this study proposes an adaptive multicore dual‐path fusion multimodel extraction of heterogeneous features for FAIMS spectral analysis model in conjunction with FAIMS small‐sample data analysis scenarios. Multinetwork complementarity is achieved through multimodel feature extraction, adaptive feature fusion module adjusts feature size and dimension fusion to heterogeneous features, and multicore dual‐path fusion can capture and integrate information at all scales and levels. The model's performance improves dramatically when performing complex mixture multiclassification tasks: accuracy, precision, recall, f1‐score, and micro‐AUC reach 98.11%, 98.66%, 98.33%, 98.30%, and 98.98%. The metrics for the generalization test using the untrained xylene isomer data were 96.42%, 96.66%, 96.96%, 96.65%, and 97.60%. The model not only exhibits excellent analytical results on preexisting data but also demonstrates good generalization ability on untrained data.