Molecular sieving membranes with uniform pore size are highly desired for carbon dioxide separation. All-silica zeolite membranes feature well-defined micropores, but the size-exclusion effect is significantly compromised by the non-selective macro-pores generated during detemplation. Here we propose a template modulated crystal transition (TMCT) approach to tune the flexibility of Decadodecasil 3R (DD3R) zeolite to prepare ultra-selective membranes for CO₂/CH₄ separation. An instantaneous overheating is applied to synchronize the template decomposition with the structure relaxation. The organic template molecules are transitionally converted to tight carbon species by the one-minute overheating at 700 °C, which are facilely burnt out by a following moderate thermal treatment. The resulting membranes exhibit CO₂/CH₄ selectivity of 157–1,172 and CO₂ permeance of (890–1,540) × 10⁻¹⁰ mol m⁻² s⁻¹ Pa⁻¹. The CO₂ flux and CO₂/CH₄ mixture selectivity reach 3.6 Nm³ m⁻² h⁻¹ and 43 even at feed pressure up to 31 bar. Such strategy could pave the way of all-silica zeolite membranes to practical applications.