Wheat (Triticum aestivum L.) is one of the most important cereals and is a major staple food in developing countries. However, in acid soils, its productivity is limited by aluminum (Al) toxicity. Wheat yield can be enhanced by modifying the spike-related traits. In order to identify quantitative trait loci (QTL) associated with Al tolerance, 167 recombinant inbred lines (RILs) derived from a cross between SeriM82 and Babax were evaluated under normal and Al stress conditions for two consecutive crop seasons. Using Composite Interval Mapping (CIM) method, 64 QTLs including 13 putative and 51 suggestive QTLs were detected for all traits. These QTLs explained 3.58–14.39% of the total variations during both the crop seasons. Using mixed model-based composite interval mapping (MCIM) method, 58 QTLs were determined to have significant additive effects, of which 21 also showed epistatic effects. Twenty-three additive QTLs had significant interaction with environment, and 35 QTLs with no additive × environment interactions (AEI) were suggested as stable. Seven pairs of 12 pairs epistatic QTLs exhibited significant interactions with environment. 16.00% of additive QTL × environment interactions (QEIs) and 71.43% of epistatic QEIs were related to Al stress with significant genetic effects increasing phenotypic values. In both method, nine QTL clusters on six LGs 2A-d, 2D, 3B, 4B, 6A-a, and 7D-a, indicated pleiotropy or gene linkage in the inheritance of spike-related traits. These results will be of great value for marker-assisted selection and QTL pyramiding in wheat breeding programs for Al tolerance, following validation in different environments and genetic backgrounds and will accelerate the understanding of the genetic relationships among spike-related traits at the molecular level.