The primary objective of this study was to assess the impact of high-intensity deep squat training integrated with various blood flow restriction (BFR) modalities on the activation of lower limb and core muscles. A randomized, self-controlled crossover experimental design was employed with 12 participants. The exercise protocol consisted of squat training at 75% of one-repetition maximum (1RM), performed in 3 sets of 8 repetitions with a 2-min inter-set rest period. This was conducted under four distinct BFR conditions: continuous low BFR (T1), intermittent medium BFR (T2), intermittent high BFR (T3), and a non-restricted control (C). Surface electromyography (EMG) was utilized to collect EMG signals from the target muscles during the BFR and squat training sessions. The root mean square (RMS) amplitude standard values were calculated for each squat set to quantify muscle activation levels, with these values expressed as a percentage of the maximum voluntary contraction (%MVC). Rating of Perceived Exertion was evaluated after each squat set, and leg circumference measurements were taken. 1) During the first two sets of deep squats, the %MVC of the vastus lateralis and vastus medialis in all compression groups was significantly higher than that in the control group (p < 0.05). Furthermore, in the first set, the %MVC of the vastus lateralis in Group T3 was significantly higher than in Group T2 (p < 0.05). In the third set, the %MVC of the vastus medialis in Groups T1 and T3 was significantly lower than in the first two sets (p < 0.05). 2) Group T1 showed an increased activation of the biceps femoris and semitendinosus muscles in the second and third sets, with %MVC values significantly greater than in the first set (p < 0.05). Group T2 only showed an increase in biceps femoris activation in the third set (p < 0.05). Group T3 significantly increased the activation of the biceps femoris and semitendinosus muscles only in the first set (p < 0.05). 3) No significant differences were observed in the changes of rectus abdominis %MVC among the groups (p > 0.05). In the first set, Group T3's erector spinae %MVC was significantly higher than the control group's; in the second set, it was significantly higher than both Group T2 and the control group's (p < 0.05). 4) After training, a significant increase in thigh circumference was observed in all groups compared to before training (p < 0.05). 5) For RPE values, Group T2's post-squat values were significantly higher than the control group's after all three sets (p < 0.05). Group T1's RPE values were also significantly higher than the control group's after the third set (p < 0.05). Groups T1, T2, and C all had significantly higher RPE values in the second and third sets compared to the first set (p < 0.05). All BFR modalities significantly enhanced the activation level of the anterior thigh muscles, with the continuous low BFR mode demonstrating a more stable effect. No significant differences were found in the activation level of the rectus abdominis among the groups. However, the intermittent high BFR mode was the most effective in increasing the activation level of the erector spinae muscles. While BFR did not further augment leg circumference changes, it did elevate subjective fatigue levels. The RPE was lowest during squatting under the intermittent high BFR condition.