Background: There is controversy regarding the effectiveness the of jailed wire technique (JWT) and jailed balloon technique (JBT) in preserving the side branch (SB) during treatment. This study compares the protective effect of JBT versus JWT on the SB ostium area in coronary bifurcation lesions using three-dimensional optical coherence tomography (3D-OCT). Methods: We obtained data from coronary heart disease patients who received OCT-guided percutaneous coronary intervention (PCI) for bifurcation lesions. The SB protection strategies were divided into JWT and JBT, with the latter further subdivided into active JBT (A-JBT) and conventional JBT (C-JBT). The primary endpoint was the SB ostium area difference measured by 3D-OCT before and after PCI. Partial correlation analysis and propensity score matching (PSM) was used to mitigate confounding biases. Results: A total of 207 bifurcation lesions from 191 patients were analyzed, including 136 lesions treated with JWT and 71 lesions treated with JBT. The SB ostium area was significantly greater in the JBT group compared to the JWT group (0.41 ± 1.22 mm2 vs. –0.25 ± 1.40 mm2, p = 0.001). Following 1:1 PSM to adjust for 60 pairs, the difference between groups was not statistically significant (0.28 ± 1.06 mm2 vs. –0.02 ± 1.29 mm2, p = 0.165). Subgroup analysis revealed that A-JBT provided superior protection in both true (0.47 ± 1.22 mm2 vs. –0.10 ± 1.10 mm2, p = 0.011) and non-true bifurcation lesions (0.56 ± 1.43 mm2 vs. –0.38 ± 1.62 mm2, p = 0.030) over JWT, while C-JBT provided protection similar to JWT. A positive partial correlation was observed between the diameter of the jailed balloon and the increase in SB ostium area (r = 0.296, p = 0.013). Conclusions: Overall, A-JBT, but not C-JBT, provided better protection in bifurcation lesions compared to JWT. The larger diameter of the jailed balloon, rather than the application of higher pressure, enhanced the SB protection.