Hi Mohit,
You can join FCI after B.Sc in Agriculture or you can join some other jobs in government or private sector. It's totally up to you. Choose whichever suits you the best. As far as FCI is concerned, there are various posts in FCI like Assistant General (AG), Accountant, Technical, Depot, Junior Engineer (civil, electrical,etc) it is not confined to agriculture related jobs. With B.Sc in Agriculture, you can apply for AG- Technical, Depot and the General posts.
The basic academic qualification for these 3 posts is bachelor's degree from a recognised university with basic computer knowledge. For AG-Technical: candidates with B.Sc agriculture,food tech, biochemistry, microbiology, zoology, etc. can apply. You can apply for only one post at a time, as per the rules.
Now the pattern of exam consists of a common preliminary exam. All posts candidates are supposed to take this exam.This exam is same for all posts in FCI. The selected candidates in this preliminary exam will be called for stage 2 exam. The paper is in CBOT (computer based online test) manner. The pattern of preliminary exam consists of total 100 questions: 35 question from reasoning section, 35 questions from maths section, and 30 questions from english section. There will also be negative marking of 0.25 marks for every wrong answer.
Also, there will be time limit for each section: 20 minutes for each section (one hour paper). After 20 minutes questions will be changed for the next section and you won't be able to change any answers later. So in 20 minutes you'll have to solve each section, no extra time is given.
The level of reasoning, english and maths can vary. Maths is upto class 10th level, more of calculative work is there. In english, you need to work on comprehensions, vocabulary and that would be very beneficial. Reasoning level can range from moderate to tough, so practice that. It will be good if you start taking mock tests. Many mock tests are available on various websites, you can practice from there or you can also join some coaching classes nearby if you need more evaluation of your preparations. You'll be able to approach the exam in a better way. 
If you want to study from books then you can refer the following books:
1. Dr. Chandresh Aggarwal's FCI TECHNICAL  latest edition.
2. Pratiyogita Kiran, for FCI exam
3. R.S Aggrawal for Quatitative aptitude (maths)
4. R.S Aggarwal for Logical Reasoning
5. Study package for FCI by Disha Publications
6. Arihant and R.S Aggarwal books for English.
Hope this helps, good luck to you!