Affine frequency division multiplexing (AFDM) is a promising chirp-assisted multicarrier waveform for future high-mobility communications. This paper is devoted to enhanced receiver design for multiple input and multiple output AFDM (MIMO-AFDM) systems. Firstly, we introduce a unified variational inference (VI) approach to approximate the target posterior distribution, under which the belief propagation (BP) and expectation propagation (EP)-based algorithms are derived. As both VI-based detection and low-density parity-check (LDPC) decoding can be expressed by bipartite graphs in MIMO-AFDM systems, we construct a joint sparse graph (JSG) by merging the graphs of these two for low-complexity receiver design. Then, based on this graph model, we present the detailed message propagation of the proposed JSG. Additionally, we propose an enhanced JSG (E-JSG) receiver based on the linear constellation encoding model. The proposed E-JSG eliminates the need for interleavers, de-interleavers, and log-likelihood ratio transformations, thus leading to concurrent detection and decoding over the integrated sparse graph. To further reduce detection complexity, we introduce a sparse channel method by approaximating multiple graph edges with insignificant channel coefficients into a single edge on the VI graph. Simulation results show the superiority of the proposed receivers in terms of computational complexity, detection and decoding latency, and error rate performance compared to the conventional ones.