Simultaneously introducing diverse genomic edits remains a challenge in crop genome engineering. We describe a twin prime editing-based knockout (TKO) system that installs stop codon clusters (SCCs) for precise translational termination with minimal in-frame mutations. TKO achieves knockout efficiencies of up to 70.5%, 58.6%, and 75.1% in rice, maize, and wheat protoplasts, respectively, and produces heritable knockout alleles in 96.8% of regenerated rice plants. In hexaploid wheat, TKO outperforms Cas9 by 4.2-fold in generating triple homeolog knockouts, largely by reducing in-frame mutations. Orthogonal TKO editors with sequence-divergent SCCs enable simultaneous knockout of up to ten genes without cross-interference. Integration of TKO with conventional prime editing establishes TRIM1 (TKO editor-enabled gene Rupture and development of Integrated Multi-type genome modification system) for simultaneous knockout and precise editing, achieving a 22.8% co-editing of four genes in rice.TRIM2 extends this capacity to kilobase-scale modifications via a PE-recombinase system, enabling a 4.9-kb insertion (1.2% efficiency) and gene knockout (up to 79.8%) in protoplasts.