We present MicroSim, a system for binary code similarity detection that represents each function as a graph built from IDA Pro Hex-Rays microcode and compares such graphs with a contrastive Siamese graph neural network (GNN). We evaluate on the TREX cross-optimization benchmark, a corpus of 849,072 function-level microcode graphs spanning optimization levels -O0 through -O3, under a strict class-disjoint split in which no function key is shared between train and test. Under this protocol, MicroSim reaches 0.9972 area under the receiver operating characteristic curve (ROC-AUC) and 0.9762 Matthews correlation coefficient (MCC), outperforming Gemini (0.9332 ROC-AUC), SAFE (0.9752), and jTrans (0.9740) retrained on the same split, as well as a structure-free Bag-of-Words (BoW) baseline (0.9484). We analyze the gap between pair classification and ranked retrieval in graph transformers, showing that Cross-domain Similarity Local Scaling (CSLS) under unified tie-resolved evaluation raises GraphGPS mean reciprocal rank (MRR) from 0.2542 to 0.2559 (R@1 = 0.1639, R@10 = 0.4561), strictly satisfying the theoretical MRR upper bound. Finally, over 5 seeds with equal compute, the pairwise cosine-embedding loss attains a slightly higher ROC-AUC (Δ = -0.0256, 95% confidence interval [-0.3282, +0.2770]), whereas the supervised-contrastive information noise-contrastive estimation (InfoNCE) loss is significantly better on thresholded classification and ranked retrieval.

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