Waste mushroom residues are often returned to fields as organic amendments. Here, we estimated the effects of the continuous applications of different spent mushroom substrates for 2 years on crop yields, soil nutrients, and heavy metals in paddy fields. The study comprised seven treatments: no fertilization (CK) and mineral NPK fertilizer (CF), as well as NPK fertilizer combined with Enoki mushroom residue (EMR50), Oyster mushroom residue (OMR50), Auricularia polytricha mushroom residue (APR50), Shiitake mushroom residue (SMR50), and Agaricus bisporus residue (ABR50). The grain yield was highest under the APR50 treatment. The short-term application of waste mushroom residue significantly increased SOC, TN, TP, and TK content relative to the CK treatment. The SOC, TP, and TK were highest under ABR50. Both total Cr and Cd contents were highest under CF treatment. The highest cumulative ecological risk was observed under OMR50 treatment. In addition, crop yield was positively correlated with SOC, TN, TP, and TP. Our results highlight that further research and innovation are needed to optimize the benefits and overcome the challenges of mushroom residue application.