Science literacy and critical thinking are very important skills for students. Some studies show the low skill of scientific literacy and critical thinking of students. Innovation in the learning process through the application of Project-Based Learning (PjBL) models in learning growth and development is needed to improve students' scientific literacy and critical thinking skills. This research aims to determine the effect of the implementation of the PjBL model on students' scientific literacy skills and critical thinking skills. This study used an experimental method with a pre-test post-test control group design. The research subjects were 128 grade XII Madrasa Aliah students who were divided into experimental and control groups. Each group consists of 64 students chosen at random. The experimental group used the PjBL learning model, while the control class continued to use the conventional learning model. The parameters measured are literacy and critical thinking skills. Data analysis of literacy skills and critical thinking is carried out through parametric statistical analysis which includes tests of normality, homogeneity, normalized gain (n-gain), and two-means comparison test. The two-means comparison test is carried out using an independent sample t-test by comparing the initial skill (pre-test results) with the final skill (n-gain). Meanwhile, the correlation of scientific literacy skill to critical thinking skill is known through correlation and regression analysis. The results showed a significant difference between the pre-test score and the n-gain score at a significant level of 95% (α = 0.05). The correlation coefficient obtained is 0.7493, which means there is a positive and strong relationship between literacy skills and critical thinking skills with the contribution of literacy skills of 56.16% to critical thinking skills. Increased literacy skill (n-gain) showed significantly different results between the experimental group and the control group. The difference of N-Gain between the experimental group and the control group was 14.25%. It shows that application of the PjBL model contributes well to improving students' scientific literacy skills.