Abstract Deep‐ultraviolet nonlinear optical (DUV NLO) crystals play a vitally important role in many scientific and technological fields, yet their rational design remains an ongoing challenge. Here, through utilizing the ordered structure design, a new KBe 2 BO 3 F 2 ‐like DUV transparent NLO crystal Cs 2 KY(B 3 O 6 ) 2 has been successfully designed and synthesized, in which we first use the largest π ‐conjugated B 3 O 6 functional groups to substitute the BO 3 to maximize the second‐harmonic generation (SHG) response and utilize the K/YO 6 connecting groups to replace two BeO 3 F groups to optimize the layer connections. Eventually, Cs 2 KY(B 3 O 6 ) 2 exhibits not only the largest SHG responses in KBe 2 BO 3 F 2 ‐like DUV borates but also the best growth rate along c axis (the strong layer‐habit along c axis has been being the greatest obstacle to prohibit the practical application of KBe 2 BO 3 F 2 and its derivative). Clearly, the substitution from BO 3 triangles to similar topological B 3 O 6 groups and from (BeO 3 F) 2 groups to similar topological K/YO 6 octahedra can better modulate the functional properties of materials in the larger scale. That results in the superior comprehensive properties of Cs 2 KY(B 3 O 6 ) 2 and makes it a promising DUV NLO crystal. Therefore, the ordered structure design provides some new insights for assembling the functional and connecting groups to rationally design materials with high‐performance.